Bioconductors: We are pleased to announce Bioconductor 2.14, consisting of 824 software packages, 200 experiment data packages, and more than 860 up-to-date annotation packages. There are 77 new software packages, and many updates and improvements to existing packages; Bioconductor 2.14 is compatible with R 3.1.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor [Amazon Machine Image] (http://bioconductor.org/help/bioconductor-cloud-ami/). Visit [http://bioconductor.org](http://bioconductor.org) for details and downloads. Contents -------- * Getting Started with Bioconductor 2.14 * New Software Packages * NEWS from new and existing packages * Packages removed from the release Getting Started with Bioconductor 2.14 ====================================== To update to or install Bioconductor 2.14: 1. Install R 3.1.0. Bioconductor 2.14 has been designed expressly for this version of R. 2. Follow the instructions at [http://bioconductor.org/install/](http://bioconductor.org/install/). New Software Packages ===================== There are 77 new packages in this release of Bioconductor. ABSSeq - Inferring differential expression genes by absolute expression differences between two groups, utilizing generalized Poisson model to account for over-dispersion across samples and heterogeneity of differential expression across genes. alsace - Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera. asmn - Performs all sample mean normalization using raw data output from BeadStudio and MethyLumiM data. ASSIGN - ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature. AtlasRDF - Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set. Basic4Cseq - Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. BEAT - Model-based analysis of single-cell methylation data BiocCheck - Bioconductor-specific package checks biosvd - The biosvd package contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures. These graphs aid in deciding which eigenfeatures and eigenassays to filter out (i.e., eigenfeatures representing steady state, noise, or experimental artifacts; or when applied to the variance in the data, eigenfeatures representing steady-scale variance). After possible removal of steady state expression, steady-scale variance, noise and experimental artifacts, and after re-applying SVD to the normalized data, a summary html report of the eigensystem is generated, containing among others polar plots of the assays and features, a table with the list of features sortable according to their coordinates, radius and phase in the polar plot, and a visualization of the data sorted according to the two selected eigenfeatures and eigenassays with colored feature/assay annotation information when provided. This gives a global picture of the dynamics of expression/intensity levels, in which individual features and assays are classified in groups of similar regulation and function or similar cellular state and biological phenotype. CAFE - Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input ccrepe - The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data. ChIPQC - Quality metrics for ChIPseq data ChIPseeker - This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak. Visualization functions are implemented to summarize genomic annotation, distance to TSS, and overlap of peaks or genes. Clomial - Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor. CNEr - Large-scale identification and advanced visualization of sets of conserved noncoding elements. COHCAP - This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. COMPASS - COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination. compcodeR - This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data and interfaces to several packages for performing the differential expression analysis. CompGO - This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files) and finally visualise and compare these enrichments using either directed acyclic graphs or scatterplots. COPDSexualDimorphism - Sexual dimoprhic and COPD differential (SDCD) analysis contrasts regression coefficients from two stratified analysis. Stratification can be done in two ways: by COPD status or by sex. For COPD-stratified analysis, SDCD analysis contrasts sexual dimorphism between cases and controls, while sex-stratified SDCD analsysis contrasts COPD differential expression pattern between males and females. The package is meant to be used in conjunction with the package limma. CopyNumber450k - This package contains a set of functions that allow CNV calling from Illumina 450k methylation microarrays. CoverageView - This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome CRISPRseek - The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. This package leverages Biostrings and BSgenome packages. DMRcate - De novo identification and extraction of differentially methylated regions (DMRs) in the human genome using Illumina Infinium HumanMethylation450 BeadChip array data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes bedGraph and plotting functions. DMRforPairs - DMRforPairs allows researchers to compare n>=2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. dualKS - This package implements a Kolmogorov Smirnov rank-sum based algorithm for training (i.e. discriminant analysis--identification of genes that discriminate between classes) and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes. EDDA - EDDA can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. ELBOW - Elbow an improved fold change test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance without assuming a normal distribution for as few as 2 biological replicates. Elbow also provides the same consistency as fold testing in cross platform analysis. Elbow has lower false positive and false negative rates than standard fold testing when both are evaluated using T testing and Statistical Analysis of Microarray using 12 replicates (six replicates each for initial and final conditions). Elbow provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance. fastLiquidAssociation - This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses. flowBin - Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers. flowCL - Semantic labelling of flow cytometric cell populations. flowCyBar - A package to analyze flow cytometric data using gate information to follow population/community dynamics flowMatch - Matching cell populations and building meta-clusters and templates from a collection of FC samples. FRGEpistasis - A Tool for Epistasis Analysis Based on Functional Regression Model gaucho - Use genetic algorithms to determine the relationship between clones in heterogenous populations such as cancer sequencing samples GeneOverlap - Test two sets of gene lists and visualize the results. geneRxCluster - Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here. GenomeInfoDb - Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order. GenomicAlignments - Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments. GenomicFiles - This package provides infrastructure for parallel queries distributed 'by file' or 'by range'. User defined map and reduce functions provide added flexibility for data combination and manipulation. GOTHiC - This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome. GSCA - GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface. iClusterPlus - Integrative clustering of multiple genomic data using a joint latent variable model INPower - An R package for computing the number of susceptibility SNPs and power of future studies massiR - Predicts the sex of samples in gene expression microarray datasets MeSHDbi - The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene- MeSH package (org.MeSH.XXX.db). loadMeSHDbiPkg import sqlite file and generate org.MeSH.XXX.db. meshr - A set of annotation maps describing the entire MeSH assembled using data from MeSH messina - Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression. metaMS - MS-based metabolomics data processing and compound annotation pipeline. metaseqR - Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way. MIMOSA - Modeling count data using Dirichlet-multinomial and beta- binomial mixtures with applications to single-cell assays. Mirsynergy - Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion. MLSeq - This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART, to RNA-Seq data. mmnet - This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome. NetPathMiner - NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation. nondetects - Methods to model and impute non-detects in the results of qPCR experiments. npGSEA - Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results. PECA - Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively. PhenStat - Package contains methods for statistical analysis of phenotypic data such as Mixed Models and Fisher Exact Test. QDNAseq - Quantitative DNA sequencing for chromosomal aberrations. Rariant - The 'Rariant' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples. Rcpi - The Rcpi package offers an R/Bioconductor package emphasizing the comprehensive integration of bioinformatics and chemoinformatics into a molecular informatics platform for drug discovery. RefNet - Molecular interactions with metadata, some archived, some dynamically obtained roar - Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments. rpx - This package implements an interface to proteomics data submitted to the ProteomeXchange consortium. sangerseqR - This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms. sapFinder - sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics. savR - Parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots. scsR - Corrects genome-wide siRNA screens for seed mediated off-target effect. Suitable functions to identify the effective seeds/miRNAs and to visualize their effect are also provided in the package. SomaticSignatures - The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). Sushi - Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures TitanCNA - Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data. trackViewer - plot ChIP-seq, RNA-seq, miRNA-seq, DNA-seq and etc NGS sequence data, especially for big files. UNDO - UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge. unifiedWMWqPCR - This packages implements the unified Wilcoxon-Mann- Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. VariantFiltering - Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minimum allele frequencies across human populations, splice site strength, conservation, etc. viper - Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms NEWS from new and existing packages =================================== Package maintainers can add NEWS files describing changes to their packages. The following package NEWS is available: ADaCGH2 ------- Changes in version 2.3.10 (2013-12-27): - Minor changes to main vignette with a new section "Why ADaCGH2 instead of a manual solution". - Change in NAMESPACE to adapt to changes in ffbase or bit (we were getting warnings of "replacing previous import by ffbase::[.ff when loading ADaCGH2"") Changes in version 2.3.9 (2013-11-28): - Minor changes to "benchmarks.pdf": consistent usage of lty and pch for figures of reading and analysis. Changes in version 2.3.8 (2013-11-26): - Minor changes to "benchmarks.pdf". Changes in version 2.3.7 (2013-11-26): - Minor changes to "benchmarks.pdf". Changes in version 2.3.6 (2013-11-24): - Help for inputToADaCGH has a more verbose section on the need to use the right mc.cores. - Made default for mc.cores to inputToADaCGH be half the number of cores. - More changes to benchmarks.pdf, including the link to all the data. Changes in version 2.3.5 (2013-11-11): - Changes in vignette: unified all benchmarking in benchmark.pdf. - Clarified help for pSegment on loadBalance and say explicitly not the default for HaarSeg. - Note versions 2.3.3 and 2.3.4 were never placed in BioC repos. Changes in version 2.3.4 (2013-11-09): - Reorganized file location for additional files (benchmarks, long- vignette). - Addedd loadBalance as an argument to the pSegment and pChromPlot functions, so that the user can choose to use load balancing-like with both forking and MPI. See additional benchmarking vignette for tables with results. Added code to the long vignette to exercise this. Changes in version 2.3.3: - Playing with clusterApplyLB. Changes in version 2.3.2 (2013-10-22): - Import aCGH and snapCGH again. Corresponding changes in Author, init.c, R code, and C code: basically, all the code taken from those packages is not here. Changes in version 2.3.1 (2013-10-20): - Added aCGH and snapCGH code: new R and C files, with minor modifications and updates (registration of routines, no partial matching of arguments, etc) - NAMESPACE and Description reflect no longer dependency on snapCGH or aCGH. - This version works, passes tests, is checked to give the same results as previous ones, etc. But never made it into BioC repos, as on 2013-10-23 I realized aCGH and snapCGH were again in BioC devel. Changes in version 2.3.0 (2013-10-20): - Version bump for new BioC devel. affxparser ---------- Changes in version 1.36.0 (2014-04-11): - The version number was bumped for the Bioconductor release version, which is now BioC v2.14 for R (>= 3.1.0). Changes in version 1.35.3 (2014-02-28): - Same updates as in release v1.34.2. Changes in version 1.35.2 (2014-02-28): - Patches to Fusion SDK based on clang v3.4. Changes in version 1.35.1 (2014-02-27): - Same updates as in release v1.34.1. Changes in version 1.35.0 (2013-10-14): - The version number was bumped for the Bioconductor devel version. AllelicImbalance ---------------- Changes in version 1.2.0: NEW FEATURES - Faster getAlleleCounts() BUG FIXES - Fixed bug in the "realCigarPosition" function, that otherwise could generate an error. alsace ------ Changes in version 0.2: - implement overlapping segments! should be a real novelty _DONE_, Oct 24 - add quality criteria in summary _DONE_, Oct 20 - complete pipeline so that the output is an intensity matrix _DONE_ - add wrapper function for a complete analysis _DONE_ Nov 20 - add some parallellization support _IN PROGRESS_: some lapply statements have been changed into mclapply but the most time-consuming step, the ALS iterations, will remain slow. Different time windows are done in parallel, but some time windows require very few iterations, others require quite a lot. In addition, the ALS output is annoying. Also the warping can be slow with many components. - add estimation of # of components annmap ------ Changes in version 1.5.10: - IMPROVED ANNMAP-121 Allow setting of WS base url for local testing Changes in version 1.5.8: - IMPROVED ANNMAP-119 as.vector=TRUE results are now named - IMPROVED ANNMAP-120 genomeToTranscriptCoords could handle coding regions Changes in version 1.5.7: - BUG Check for uniqueness in transcriptToCodingExon, transcriptToCodingRange, transcriptToUtrExon and transcriptToUtrRange Changes in version 1.5.6: - NEW Added transcriptToUtrExon - IMPROVED Sequence removed from transcriptToCodingExon Changes in version 1.5.5: - IMPROVED ANNMAP-115 Added method geneToGeneRegionTrack to generate a list of Gviz GeneRegionTrack elements that can be passed to plotTracks Changes in version 1.5.4: - BUG ANNMAP-118 transcriptToCodingRange( ..., end='3' ) returns whole transcript for untranslated transcripts. - IMPROVED ANNMAP-114 Added additional logging when using webservice - IMPROVED ANNMAP-116 Introduce function(s) to calculate the coding length of a gene(s) - See: ?nonIntronicGeneLength and ?nonIntronicTranscriptLength. Changes in version 1.5.3: - IMPROVED ANNMAP-114 Added additional logging when using webservice - IMPROVED ANNMAP-113 Added documentation to cookbook for webservice - IMPROVED webservice json to data.frame speed improvements AnnotationDbi ------------- Changes in version 1.26: NEW FEATURES and API changes - Support for new schemaless chip packages to allow more flexible suport of non-model organisms in chip packages. - Support for Inparanoid8 objects which contain data from the most recent release of inparanoid. These objects will be available through the AnnotationHub. BUG FIXES AND CODE MAINTENANCE - PFAM and PROSITE mappings are going away! This is because these mappings are tied to the now long defunct IPI ids. Don't worry we have you covered. These ids will still be available with select(), the mappings are just bad because they can't exist without IPI ids (which we can no longer get). So for the next release if you try to use these mappings you will be warned about it. After that, you need to have made the switch to select(). * * * 1.24.x SERIES NEWS * * * AnnotationHub ------------- Changes in version 1.4.0: NEW FEATURES - Add display,AnnotationHub-method using shiny - Adds support for Inparanoid8 objects (which in turn support select, keys, columns and keytypes) - Adds local metadata caching that dramatically improves performance SIGNIFICANT USER VISIBLE CHANGES - metadata argument 'columns' replaces deprecated 'cols' BUG FIXES - metadata() returns only information on current hub elements aroma.light ----------- Changes in version 2.0.0 (2014-04-11): - The version number was bumped for the Bioconductor release version, which is now BioC v2.14 for R (>= 3.1.0). Changes in version 1.99.3 (2014-03-31): - Bumped the version such that the next release will be 2.0.0. BaseSpaceR ---------- Changes in version 1.7: NEW FEATURES - Improved API design and a cleaner representation of the BaseSpace Data Model. - New count<resource> methods. These methods should be used to get the number of instances of a particular resource which are visible under the current scope. For example, the total number of Samples within a Project. Or the total number of Files for a given AppResults. - Improved authentication process. One can now seamlessly used the R SDK from with Native Apps or Web Apps. New 'AppSessionAuth' class to handle the authentication in this cases. It extends the 'AppAuth' class, by keeping track of the AppSession Id. User-level constructors: 'authWebClient()' and 'authNativeClient()' generator .AppSessionAuth(). - New mechanism for handling the BaseSpace server responses. 'ResponseStatus' class is now used for tracking the HTTP/server response status and integrated in the 'AppAuth' interface. 'x$showResponse()' can now be used to print the (JSON) body of the last response from the server. - Integration with some Bioconductor data structures. BAM data from BaseSpace can now be easily map to 'BamFile' objects. SIGNIFICANT USER-VISIBLE CHANGES - 'authenticateClient()' function remove and replaced by 'authWebClient()' and 'authNativeClient()'. 'AppAuth' instances are used for desktop Apps only. BUG FIXES - Minor bug fixes with the authentication process. - Method dispatchment now works as intended for 'listFiles' and 'Files'. BiGGR ----- Changes in version 1.1.4: - Updated vignette. Equality constraints on GABA shunt and pentose phosphate pathway fluxes are now used in FBA and ensemble simulations. Changes in version 1.1.3: - Updated vignette and bibtex file. FBA and ensemble sampling are now done with integration of brain metabolite uptake measurement data. - Added new function 'sampleFluxEnsemble' which can be used to generate a posterior distribution of flux vectors with respect to measuerement error in certain fluxes. An example of 'sampleFluxEnsemble' has been added to the package vignette. - Added LIM model file 'Glycolysis_TCA.LIM' to the examples directory. This file contains the model which is build in the examples. - Fixed warnings in functions buildSBMLFromReactionIDs and createLIMFromSBML to seperate missing identifiers with a comma. BiocInstaller ------------- Changes in version 1.14.0: NEW FEATURES - biocUpdatePackages updates installed packages and their dependencies. BiocParallel ------------ Changes in version 0.5.5: NEW FEATURES - multicoreWorkers() determines the number of workers based on operating system (Windows: 1), user preference (via the global option options(mc.cores=...)), or system capability (detectCores()). - bpparam() selects a default BiocParallelParam, from global options or, if that fails, the most recently registered() back-end. SIGNIFICANT USER-VISIBLE CHANGES - Rename argument controlling resumption on error as BPRESUME - Default to parallel back-end (multicore on non-Windows; snow on Windows). BUG FIXES - bpvec,ANY,MulticoreParam-method with fewer tasks than cores evaluates only the cores for which tasks are defined. Changes in version 0.5.2: NEW FEATURES - mclapply(), pvec() require only length, [, and (for mclapply) [[. - pvectorize() creates a parallel version of its vectorized function argument. - MulticoreParam, SnowParam, DoparParam (foreach-derived), SerialParam to parameterize back-ends. - bplapply, bpvec as parallel evaluation models. - bpstart, bpstop, bpisup for back-end management. - bpvec has a new argument AGGREGATE, a function to specify how results are to be combined. - Support for BatchJobs back-end added, via GSOC Michel Lang. SIGNIFICANT USER-VISIBLE CHANGES - BPPARM is now used as the argument name for passing BiocParallelParam instances to functions. - bplapply and bpvec now only dispatch on X and BPPARAM. BiocStyle --------- Changes in version 1.2.0: USER VISIBLE CHANGES - Remove dependency on 'helvet' LaTeX package to allow for the same font both in Sweave and knitr - Improve package vignette by adding paragraphs about building vignettes and using bibliography - knitr chunk_opts error=FALSE by default, so failures during vignette processing are signaled to R CMD build and R CMD check - Name-mangle \comment mark-up to avoid conflicts with other LaTeX styles - Introduce \bioctitle to allow for full and short (header) titles - Add BiocStyle::latex option 'use.unsrturl=TRUE' to use the 'unsrturl' bibliography style by default BUG FIXES - Avoid use of 'titling' LaTeX package to circumvent the conflict w/ \footnote in \author biomvRCNS --------- Changes in version 1.3.3: NEW FEATURES - updates in package vignette BUG FIXES - remove limitation of maximum typecode in the plot, now using rainbow() Changes in version 1.3.2: BUG FIXES - fix the returned posterior p bsseq ----- Changes in version 0.11: - Converted to using Authors at R in the DESCRIPTIOn file. - plotRegion did not respect the col/lty/lwd argument if given explicitely as opposed to through pData(). Reported by Karen Conneely <kconnee at="" emory.edu="">. - Fixed an issue introduced by the previous change (to plotRegion). Reported (with a fix) by Tim Triche Jr <tim.triche at="" gmail.com="">. - Fixed a serious bug in collapseBSseq reported by Julien Roux <jroux at="" uchicago.edu="">: it would use the Meth values instead of Cov for the final object's Cov. However, this will result in the return object having a methylation of 100 percent across all loci, so hopefully users will have seen this for themselves. - Fixed a bug in combineList which made combineList use "slow" code even in a special case where a faster shortcut was possible. This bug fix does not change the output of the function under any input, it only makes it faster. Reported by Julien Roux <jroux at="" uchicago.edu="">. bumphunter ---------- Changes in version 1.3.5: - nearestgene() now loads TT.rda into the local environment - known_transcripts(), and consequently matchGenes(), was yielding mostly NA for the Refseq / 'annotation' column (iff there were multiple refseq ids for the given Entrez/Gene id) - Fixed data/TT.rda, as the new value of known_transcripts() Changes in version 1.3: - Fixed NAMESPACE issues. CAFE ---- Changes in version 0.99.2: - Code and man files are now limited to 80 character width per line - Code now uniformly uses 4-space indentation - Vignette now uses BiocStyle style Changes in version 0.99.1: - fixes a bug that gave an error when plotting with idiogram=TRUE. This was due to an update in the ggbio package that broke CAFE - CAFE can now be used with species other than human It is no longer limited to 22 autologous chromosomes CAMERA ------ CHANGES IN VERSION 1.19.1 * Fixed bug in the generateRules function, where in the negative mode rules with polycharged positve ions are not created CellNOptR --------- Changes in version 1.10.0 (2014-03-13): - BUG FIX * typos leading to failure fixed in cutCNOlist * typos leading to failure in CNOlist if variance were provided - CHANGES * Changed warning into errors in readMIDAS and checkSignals functions - NEW FEATURES * self loop can be read from the SIF files * readSBMLQual do not need to add dummy nodes anymore ChemmineOB ---------- Changes in version 1.2.0: NEW FEATURES - SMARTS search ChemmineR --------- Changes in version 2.16.0: NEW FEATURES - SMARTS Search availible through ChemmineOB - Folding of FPset objects - Support for SQL database updates by compound name - Coordinate re-generation via ChemmineOB improves structure rendering chimera ------- Changes in version 1.5.2: NEW FEATURES - prettyPrint function was added to generate a table delimited file output form a list of fSet objects. ChIPpeakAnno ------------ Changes in version 2.11.4: NEW FEATURE - Add selection of 'shortestDistance' to output parameter of annotatePeakInBatch. Changes in version 2.11.3: NEW FEATURE - Improved efficiency of annotatePeakInBatch. ChIPQC ------ Changes in version 1.0.0: - Initial release. cisPath ------- Changes in version 1.3.3: - improvements Changes in version 1.3.1: - documentation improvements cleanUpdTSeq ------------ Changes in version 1.1.3: NEW FEATURES - No changes classified as "new features" (package under active development) BUG FIXES - Fix the bugs 'match' requires vector arguments when using %in% Changes in version 1.1.2: NEW FEATURES - Add citation BUG FIXES - No changes classified as 'bug fixes' (package under active development) Changes in version 1.1.1: NEW FEATURES - Re-name the inst/doc directory to vignettes BUG FIXES - No changes classified as 'bug fixes' (package under active development) Changes in version 1.1.0: NEW FEATURES - New package released in bioconductor BUG FIXES - No changes classified as 'bug fixes' (package under active development) cleaver ------- Changes in version 1.1.8 (2014-03-26): - Fix missedCleavages>1. - Add argument "unique". - Add methods, Biostrings, IRanges to NAMESPACE. Changes in version 1.1.7 (2014-03-25): - Typo in the manual page. Changes in version 1.1.5 (2014-02-25): - Using AAStringSetList constructor for list of characters instead of creating a lot of AAStringSets dramatically decreases running time for cleave,AAStringSet-method. Changes in version 1.1.4 (2013-12-20): - tests: - move tests into tests/testthat to adapt to testthat 0.8 and new CRAN policy. Clomial ------- Changes in version 0.99.0 (2014-02-11): - Under review by Bioconductor. - Created. clonotypeR ---------- Changes in version 1.2.0: NEW FEATURES - Added a ?long? option to yassai_identifier(), where every amino acid is represented. This solves the problem of ID collisions, where a single identifier could be produced by two different clonotypes. - Added a new option to clonotype_table() for randomly sampling libraries. - Added a new mode to common_clonotypes() for calculating the abundance relatively to one library. - Unified the syntax of common_clonotypes() and unique_clonotypes(). BUG FIXES - Removed infinite loop in yassai_identifier() when the germinal V sequence was completely absent from the CDR3. - Corrected output bug where ?integer(0)? was returned if the V?J boundary was a codon boundary. - yassai_identifier(): properly encode the names of the V and J segments. clusterProfiler --------------- Changes in version 1.11.3: - now plotting compareClusterResult support scale the dot size by geneRatio, and it is now setting as default. <2014-01-14, Tue> - The original default parameter by="percentage" is now changing to "rowPercentage" <2014-01-14, Tue> Changes in version 1.11.2: - remove viewKEGG function <2013-11-12, Tue> - In vignette, illustrates how to visualize KEGG pathway using use pathview package. <2013-11-12, Tue> CNAnorm ------- 1.9.2: Added function CNAnormWorkflow Added window weighting (for segmentation) depending on dispersion. Fixed a bug that made plotGenome crash if the interval of interest had no valid values. Changed vignette to better reflect typical usage and defined basic and advanced use. codelink -------- Changes in version 1.32.0: - Minor fixes to documentation. - Dropped the old term "Bioarray" (originally used for the first Codelink platform) from the DESCRIPTION file. COMPASS ------- Changes in version 0.9.0: - First release. compcodeR --------- 0.99.2: Bug fixes 0.99.1: improved documentation of the compData class 0.2.0: more examples, checks and error messages 0.2.0: more options for providing user-specified values in the data simulation 0.2.0: changed the range of the color palette in the Spearman correlation plots to [-1,1] deepSNV ------- Changes in version 1.99.3 (2013-07-25): Updates - A few changes to shearwater vignette - Renamed arguments pi.gene and pi.backgr in makePrior() Bugfixes - Fixed bug in bf2Vcf() when no variant is called Changes in version 1.99.2 (2013-07-11): Updates - Updated CITATION - Added verbose option to bam2R to suppress output - Changed mode() to "integer" for value of loadAllData() Bugfixes - Fixed bug when only one variant is called in bf2Vcf() Changes in version 1.99.1 (2013-06-25): Updates - Using knitr for prettier vignettes - Including shearwater vignette Bugfixes - fixed issues with deletions in bf2Vcf() - makePrior() adds background on all sites Changes in version 1.99.0 (2013-04-30): Updates - New shearwater algorithm - Including VCF output through summary(deepSNV, value="VCF") DESeq2 ------ Changes in version 1.4.0: - *** USAGE NOTE *** Expanded model matrices are now used when betaPrior = TRUE (the default). Therefore, level comparison results should be extracted using the 'contrast' argument to the results() function. Expanded model matrices produce shrinkage of log fold changes that is independent of the choice of base level. Expanded model matrices are not used in the case of designs with an interaction term between factors with only 2 levels. - The order of the arguments 'name' and 'contrast' to the results() function are swapped, to indicate that 'contrast' should be used for the standard comparisons of levels against each other. Calling results() with no arguments will still produce the same comparison: the fold change of the last level of the last design variable over the first level of the last design variable. See ?results for more details. - The DESeq() function will automatically replace count outliers flagged by Cook's distance when there are 7 or more replicates. The DESeq() argument 'minReplicatesForReplace' (default 7) is used to decide which samples are eligible for automatic replacement. This default behavior helps to prevent filtering genes based on Cook's distance when there are many degrees of freedom. Changes in version 1.3.58: - Added a list() option to the 'contrast' argument of results(). See examples in ?results. Changes in version 1.3.24: - rlogTransformation() gains an argument 'fast', which switches to an approximation of the rlog transformation. Speed-up is ~ 2x. - A more robust estimator for the beta prior variance is used: instead of taking the mean of squared MLE betas, the prior variance is found by matching an upper quantile of the absolute value of MLE betas with an upper quantile of a zero-centered Normal distribution. Changes in version 1.3.17: - It is possible to use a log2 fold change prior (beta prior) and obtain likelihood ratio test p-values, although the default for test="LRT" is still betaPrior=FALSE. Changes in version 1.3.15: - The DESeq() function will automatically replace count outliers flagged by Cook's distance when there are 7 or more replicates. The DESeq() argument 'minReplicatesForReplace' (default 7) is used to decide which samples are eligible for automatic replacement. This default behavior helps to prevent filtering genes based on Cook's distance when there are many degrees of freedom. - The results() function produces an object of class 'DESeqResults' which is a simple subclass of 'DataFrame'. This class allows for methods to be written specifically for DESeq2 results. For example, plotMA() can be called on a 'DESeqResults' object. Changes in version 1.3.12: - Added a check in nbinomWaldTest which ensures that priors on logarithmic fold changes are only estimated for interactions terms, in the case that interaction terms are present in the design formula. Changes in version 1.3.6: - Reduced the amount of filtering from Cook's cutoff: maximum no longer includes samples from experimental groups with only 2 samples, the default F quantile is raised to 0.99, and a robust estimate of dispersion is used to calculate Cook's distance instead of the fitted dispersion. Changes in version 1.3.5: - New arguments to results(), 'lfcThreshold' and 'alternativeHypothesis', allow for tests of log fold changes which are above or below a given threshold. - plotMA() function now passes ellipses arguments to the results() function. DEXSeq ------ Changes in version 2014-03-21: - Major code revisions: the ExonCountSet object was deprecated and substituted by the DEXSeqDataSet class, a subclass of the DESeqDataSet. - DEXseq now uses the DESeq2 package as internal engine and backbone for all analyses - All functions and methods for the ExonCountSet object were replaced by new functions - DEXSeq is now better integrated with other Bioconductor packages - We now use knitr to build the vignette DiffBind -------- Changes in version 1.10.0: - Counting * New: option to compute summits * New: option to center peaks with fixed width around summits * New: scores for summits (height, position) and CPM for TMM values * New: filter reads by mapping quality (mapQCth) * New: support for PE bam data using summarizeOverlaps * Remove: bCalledMask (now always TRUE) * Change: insertLength to fragmentSize * Add: fragmentSize can be a vector with a size for each sample * Change: fragmentSize default is 125 bp - Plotting * Change: colors based on CRUK color scheme * PCA plots * New: legend * New: label parameter for adding text labels of points in 2D plot * Venn diagrams * New: plot overlaps of differentially bound sites by specifying contrasts, thresholds etc. * New: able to return overlapping peaksets as GRanges directly * New: able to generate new DBA object consisting of overlapping peaks * New: labelAttributes for controlling default labels * New: default main and sub titles * Heatmaps * Fix: don?t plot column vector for attributes where every sample has a different value - General * New: add attribute value: DBA_ALL_ATTRIBUTES * Change: SN (signal/noise) to FRIP (fraction of reads in peaks) * Change: ?Down? to ?Loss? and Up? to ?Gain? * Vignette * Change: vignette uses BiocStyles and dynamically generated figures * Change: example data based on hg19 instead of hg18 * Change: example reads from bam files instead of bed files * New: section on using DiffBind and ChIPQC together * New configuration defaults options (DBA$config): * Metadata name strings: ID, Tissue, Factor, Condition, Treatment, Caller * th: significance threshold * bUsePval * fragmentSize * mapQCth: filter reads by mapping quality * fragments (for summarizeOverlaps) - Bugs/Issues * Fix: bRemoveDuplicates had some unpredictable behaviour * Fix: chrN_random were being counted against chrN * Disable: tamoxifen_GEO.R doesn?t work after SRA changed format of archived data easyRNASeq ---------- Changes in version 1.99.3: - Replicated the bug fixing of version 1.8.8. Changes in version 1.99.2: - Added missing imports Changes in version 1.99.1: - Fixed a bug in the getBamFileList function that prevented reporting accurate error/warning messages. - Updated the package dependencies. Changes in version 1.99.0: - Ported the final changes from the Git repository that make the simpleRNASeq function functional. - Bumped the version number to 1.99 as these are major changes and hence next Bioc release will have easyRNASeq 2.0.0. Changes in version 1.9.7: - Same as release 1.8.7 change. Changes in version 1.9.6: - Ported changes from the Git repository including further class refinements and unit testing. Changes in version 1.9.5: - Automatic version number bump by Bioc Changes in version 1.9.4: - Mirrored changes in version 1.8.6 Changes in version 1.9.3: - Mirrored changes in version 1.8.5 Changes in version 1.9.2: - Ported version 1.8.4 changes to the development version - Started to import new classes from the git repository as part of the package main function re-implementation Changes in version 1.9.1: - Change from Bioc to insert GenomicAlignments Changes in version 1.9.0: - No changes, new development version EBImage ------- Changes in version 4.6.0: NEW FEATURES - 'toRGB' function for convenient grayscale to RGB conversion - 'luminance' mode in 'channel' for luminance-preserving RGB to grayscale conversion SIGNIFICANT USER-VISIBLE CHANGES - Performance improvements to: 'Image', 'is.Image', 'readImage', 'writeImage', 'show', 'normalize', 'getFrame', 'selectChannel', 'rgbImage', 'colorLabels', 'flip'/'flop' - Reduced memory footprint of 'readImage' - When called on an 'Image' object, 'as.Image' returns its argument rather than the Grayscale-coerced copy - 'displayRaster' sets 'par$usr' coordinates to image pixel coordinates easing up plot annotation BUG FIXES - 'getFrame', 'getNumberOfFrames' and 'colorLabels' support multi- dimensional images - Proper handling of multi-dimensional character arrays by the 'Image' constructor - Fixed 'getFrame' and 'combine' in case of single-channel Color Images - Fixed color mode check in 'validImageObject' - Proper 'fg.col' and 'bg.col' color handling in 'tile' - Updates to documentation EDASeq ------ Changes in version 1.9: - Added method plotRLE for Relative Log Expression (RLE) plots. EDDA ---- Changes in version 0.99.2: SIGNIFICANT USER-VISIBLE CHANGES - Put "NEWS.Rd" in EDDA/. - Change biocViews to DESCRIPTION file. - Modify DESCRIPTION and NAMESPACE file. - move the data to EDDA/inst/extdata. Changes in version 0.99.1: SIGNIFICANT USER-VISIBLE CHANGES - Put "EDDA.Rnw" in EDDA/vignettes. - Remove "library("EDDA");" in file man/EDDA-package.Rd. - Clean up pre-defined tempates in man files. - Use TRUE instead of T and FALSE instead of F. - Clean R code by breaking code less 80 characters, removing tabs and using indent by a multiple of 4 spaces. NEW FEATURES - Add biocViews to DESCRIPTION file. - Add KEYWORDS for each function man file. - Add "NEWS.Rd" in EDDA/inst/. Changes in version 0.99.0: SIGNIFICANT USER-VISIBLE CHANGES - Submit EDDA edgeR ----- Changes in version 3.6.0: - Improved treatment of fractional counts. Previously the classic edgeR pipeline permitted fractional counts but the glm pipeline did not. edgeR now permits fractional counts throughout. - All glm-based functions in edgeR now accept quantitative observation-level weights. The glm fitting function mglmLS() and mglmSimple() are retired, and all glm fitting is now done by either mglmLevenberg() or mglmOneWay(). - New capabilities for robust estimation allowing for observation- level outliers. In particular, the new function estimateGLMRobustDisp() computes a robust dispersion estimate for each gene. - More careful calculation of residual df in the presence of exactly zero fitted values for glmQLFTest() and estimateDisp(). The new code allows for deflation of residual df for more complex experimental designs. - New function processHairpinReads() for analyzing data from shRNA-seq screens. - New function sumTechReps() to collapse counts over technical replicate libraries. - New functions nbinomDeviance() and nbinomUnitDeviance. Old function deviances.function() removed. - New function validDGEList(). - rpkm() is now a generic function, and it now tries to find the gene lengths automatically if available from the annotation information in a DGEList object. - Subsetting a DGEList object now has the option of resetting to the library sizes to the new column sums. Internally, the subsetting code for DGEList, DGEExact, DGEGLM, DGELRT and TopTags data objects has been simplified using the new utility function subsetListOfArrays in the limma package. - To strengthen the interface and to strengthen the object-orientated nature of the functions, the DGEList methods for estimateDisp(), estimateGLMCommonDisp(), estimateGLMTrendedDisp() and estimateGLMTagwiseDisp no longer accept offset, weights or AveLogCPM as arguments. These quantities are now always taken from the DGEList object. - The User's Guide has new sections on read alignment, producing a table of counts, and on how to translate scientific questions into contrasts when using a glm. - camera.DGEList(), roast.DGEList() and mroast.DGEList() now include ... argument. - The main computation of exactTestByDeviance() now implemented in C++ code. - The big.count argument has been removed from functions exactTestByDeviance() and exactTestBySmallP(). - New default value for offset in dispCoxReid. - More tolerant error checking for dispersion value when computing aveLogCPM(). - aveLogCPM() now returns a value even when all the counts are zero. - The functions is.fullrank and nonEstimable are now imported from limma. eiR --- Changes in version 1.4.0: NEW FEATURES - eiCluster can now cluster subsets of database - use new features in ChemmineR to store duplicate descriptors only once. - embedded descriptors now stored in database and the matrix file is written out only as needed by LSH to create an index. UPGRADING - Database schema changes make this version incompatible with version 1.2 an earlier. Existing databases will need to be re-loaded. ensemblVEP ---------- Changes in version 1.4.0: NEW FEATURES - VEPParam is now VIRTUAL with subclasses VECParam67 and VEPParam73 - Add helpers currentVEP() and supportedVEP() - Add VEPParam75 class MODIFICATIONS - Modify VEPParam to support API versions 67 and 73 - Add slots 'scriptPath' and 'version' to VEPParam - New man page for runtime options - Update biocViews terms FGNet ----- Changes in version 2.0: NEW FEATURES - The networks can now be plotted for terms in addition to genes. - In the report, clicking on the plots allows to see the plot at full size next to the terms table (if the screen resolution allows it). - ToMatrix(): Added arguments 'key' (to choose either genes or terms) and 'removeFiltered' terms. Renamed main argument (geneTermSets) to 'results'. - IntersectionNetwork() shows a warning if there is no intersection. Added argument 'plotAllMg' to allow choosing wether to plot unconnected metagroups or not. - FunctionalNetwork() changed the two main arguments to a single one, which is the raw output from toMatrix() (a list with names: c("metagroupsMatrix", "gtSetsMatrix", "filteredOut")). Added arguments: 'eColor' to provide the edges color, and 'weighted' to draw the edge width according to the number of shared gene-term sets. - Reports: Added argument 'downloadGOtree' to allow choosing wether to download the go term trees png (slower) or just provide the link to the web tool. BUG FIXES - functionalNetwork() now correctly writes either "cl" or "mg" in the legend Changes in version 1.3.1: NEW FEATURES - adjMatrix() has been renamed to toMatrix() - GO png trees are now automatically downloaded when generating the report - functionalNetwork: metagroup/cluster legend order has been changed to alphabetical BUG FIXES - Minor bug fixes flipflop -------- Changes in version 1.1.6: NEW FEATURES - Add 'expected.counts' in the output objects. It gives the expected raw count (ie number of mapped fragments) for each predicted transcripts. This information is also available in the output gtf file. Changes in version 1.1.4: NEW FEATURES - Add a 'OnlyPreprocess' option for performing only the pre-processing step of the input sam file. This step writes two files: one file named 'prefix.instance' and one other named 'prefix.totalnumread', where 'prefix' is the prefix of the input sam file. The 'prefix.instance' file can then be given to the option 'preprocess.instance' and the total number of mapped reads is stored in the 'prefix.totalnumread' file. - Allow to give 'NN' (total number of mapped fragments) even when using the sam file as input. This can be used to run flipflop in parallel on parsed sam files with the same NN constant. USER-LEVEL CHANGES - Handle '~' in input paths with path.expand function. - Give a more detailed R output with the read count. MINOR CHANGES - Do not write individual Coverage into the pre-processing file anymore ie, the .instance file. (in practice comments lines in readgroup.cpp, part 'toStream') Changes in version 1.1.2: BUG FIXES - Switch from GRangeList to a regular list as the number of metadata columns could not vary in GRangeList. fmcsR ----- Changes in version 1.6.0: NEW FEATURES - Added timeout option - Allow parallel execution for batch computations FRGEpistasis ------------ Changes in version 0.99.5: - Added FDR control Changes in version 0.99.4: - Completed the man pages - Added the NEWS file - Updated the DESCRIPTION file - Completed the vignette - Updated the genotype file format Changes in version 0.99.3: - Corrected the biocViews Changes in version 0.99.1: - Added FRGEpistasis vignette gage ---- Changes in version 2.12.1: - remove pathview from the imports list for easier installation and loading. gCMAP ----- Changes in version 1.7.2: - CHANGE: Helper functions KEGG2cmap, reactome2cmap, wiki2cmap and go2cmap have two additional parameters, min.size and max.size, restricting the output to gene sets containing members within the specified range. - CHANGE: Method camera_score now outputs correlations in column 'effect'. - BUGFIX: Correct numbers of annotated genes are now returned for each set. Changes in version 1.7.1: - CHANGE: Vignettes are now stored in vignettes directory. gCMAPWeb -------- Changes in version 1.3.2: - BUGFIXMoved the 'Rook' package from 'Imports' to 'Depends' Changes in version 1.3.1: - CHANGEVignettes are now stored in vignettes directory. geNetClassifier --------------- Changes in version 1.3.1: NEW FEATURES - plotAssignments: Optimized speed and changed background color to blue. Added argument pointSize. - plotExpressionProfiles: Added argument sampleColors. BUG FIXES - Added RUnit and BiocGenerics to "Suggests" to avoid R CHECK warnings - Import methods, ebarrays and emfit in namespace to avoid R CHECK warnings - plot.GenesNetwork is now completelly equivalent to plotNetwork (same default arguments) GenomeInfoDb ------------ Changes in version 0.99.14: SIGNIFICANT USER-VISIBLE CHANGES - rename: package: Seqnames --> GenomeInfoDb supportedStyles -> genomeStyles makeSeqnameIds --> rankSeqlevels (add to export) seqnamesOrder --> orderSeqlevels extractSeqnameSet -> extractSeqlevels extractSeqnameSetByGroup -> extractSeqlevelsByGroup findSequenceRenamingMaps --> mapSeqlevels seqnamesInGroup --> seqlevelsInGroup seqnamesStyle --> seqlevelsStyle "seqnameStyle<-" --> "seqlevelsStyle<-" Changes in version 0.99.7: SIGNIFICANT USER-VISIBLE CHANGES - rename: isSupportedSeqnames -> .isSupportedSeqnames supportedSeqnameStyles -> .supportedSeqnameStyles supportedSeqnameMappings -> .supportedSeqnameMappings isSupportedSeqnamesStyle -> .isSupportedSeqnamesStyle Changes in version 0.99.6: NEW FEATURES - add new functions() seqnamesInGroup which will take a character vector of chromosomes and return the chromosomes specified by the group parameter supplied by the user. The user can also give the species and the style. seqnamesOrder() internally calls Herve's function makeSeqnameIds() - add seqnameStyles generic and method from GenomicRanges SIGNIFICANT USER-VISIBLE CHANGES - rename: testSeqnames -> isSupportedSeqnames - move SeqnamesStyle generic from GenomicRanges and define a new method which works on a character vector. DEPRECATED AND DEFUNCT - deprecate listAllSupportedStylesBySpecies(), listAllSupportedSeqnameStyles(), supportedOrganisms() supportedSeqnameMappingsWithGroup() DEPRECATED AND USED INTERNALLY(NOT EXPORTED - deprecate supportedSeqnameMappings(), supportedSeqnameStyles(), isSupportedSeqnamesStyle(),issupportedSeqnames() Changes in version 0.99.1: SIGNIFICANT USER-VISIBLE CHANGES - The Seqnames package will have functions which will be moved from AnnotationDbi , GenomicRanges - List of 9 functions moved from AnnotationDbi supportedSeqnameMappings, findSequenceRenamingMaps, supportedSeqnameStyles, supportedSeqnames, extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle, listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles. - makeSeqnameIds moved from GenomicRanges - keepStandardChromosomes moved from GenomicRanges - rename: keepStandardChromosomes -> keepChromosomes NEW FEATURES - added new functions: supportedOrganisms() supportedSeqnameMappingsWithGroup() extractSeqnameSetByGroup() GenomicAlignments ----------------- Changes in version 0.99: NEW FEATURES - coverage,BamFile-method uses yieldSize to iterate through large files. - coverage,character-method calculates coverage from a BAM file. GenomicFiles ------------ Changes in version 1.0.0: NEW FEATURES - First release of GenomicFiles package GenomicRanges ------------- Changes in version 1.16.0: NEW FEATURES - Add "subset" method for SummarizedExperiment objects. - Allow DataFrame in SummarizedExperiment assays. - Add 'use.mcols' arg (FALSE by default) to the granges(), grglist(), and rglist() generics (a.k.a. the range-squeezer generics). - Add coercion method from GRangesList to RangesList. - Add score() setter for GRangesList objects. - findOverlaps(..., type="within") now works on circular chromosomes. - Add 'ignore.strand' arg to "sort" method for GRanges objects. - Support subsetting of a named list-like object *by* a GenomicRanges subscript. - Support sort(granges, by = ~ score), i.e., a formula-based interface for sorting by the mcols. SIGNIFICANT USER-LEVEL CHANGES - Move many functionalities to the new GenomicAlignments package: - The GAlignments, GAlignmentPairs, and GAlignmentsList classes. - The qnarrow() generic and methods. - The "narrow" and "pintersect" methods for GAlignments and GAlignmentsList objects. - The low-level CIGAR utilities. - The "findOverlaps" methods for GAlignment* objects. - The summarizeOverlaps() generic and methods, and the "Counting reads with summarizeOverlaps" vignette. - findCompatibleOverlaps() and countCompatibleOverlaps(). - The findSpliceOverlaps() generic and methods. - The "overlap encodings" stuff i.e. the "encodeOverlaps" method for GRangesList objects, flipQuery(), selectEncodingWithCompatibleStrand(), isCompatibleWithSplicing(), isCompatibleWithSkippedExons(), extractSteppedExonRanks(), extractSpannedExonRanks(), extractSkippedExonRanks(), and extractQueryStartInTranscript(), and the "OverlapEncodings" vignette. - Rename 'with.mapping' arg -> 'with.revmap' in "reduce" methods. The old arg name is still working but deprecated. - Move makeSeqnameIds() function to the new GenomeInfoDb package and rename it rankSeqlevels(). The old name is still working but deprecated. - The "strand" methods now perform stricter checking and are guaranteed to always return a factor (or factor-Rle) with the "standard strand levels" and no NAs. Or to fail. BUG FIXES - Tweaks and fixes to various "strand" methods: - Methods for character vectors and factors do not accept NAs anymore (they raise an error). - Methods for integer and logical vectors map NAs to * (instead of NA). - Method for Rle objects now also works on character-, factor-, and integer-Rle objects (in addition to logical-Rle objects). genoset ------- Changes in version 1.16.0: NEW FEATURES - cn2lr now has methods for vector, matrix, and DataFrame (of Rle) and allows you to center your log2ratio values on 2 copies, or on a specified 'ploidy' for your sample. DEPRECATED AND DEFUNCT - The BAFSet and CNSet classes have moved from deprecated to defunct. These classes only added getter/setter methods for baf/lrr/cn. Since these only cover some possible assayDataElements, it is better to use x[i,j,k], where k is the name of an assayDataElement. - All RangedData-related things have now progressed to defunct. Please use GRanges for locData and everywhere else. Since the genoset package provides a common API for GenoSet, GRanges, and RangedData, I hope this will be a simple change for everyone. - sampleNames and featureNames are now *un-deprecated*. Feel free to use them. They just call colnames and rownames, respectively. I have defined my own rownames and colnames functions. The eSet ones seem to do a lot of extra work, and the getter versions read from the first assayDataElement, rather than pData and fData. I changed to the latter, so BigMatrix assayDataElements will remain untouched until you really mean to access them. GGBase ------ Changes in version 3.25.1: - plot_EvG will, for probeId() first argument, attempt to translate to gene symbol for y axis labeling GGtools ------- Changes in version 4.11: - appraise and calfig are provided to foster evaluation of eQTL-based GWAS hit predictions - cisAssoc has been added to obtain assay data from SummarizedExperiment and variants from VCF - CisConfig instances keepMapCache now defaults to TRUE - for naming symmetry we now have cisScores and transScores operating on CisConfig and TransConfig instances respectively - Added transeqByCluster() for nested concurrency for trans searches - Added TransConfig class to control trans searches, and modified transScores accordingly - Added hmm878, chromatin map of GM12878 for assessment of chromatin state enrichments - Added gffprocess(), of use when All.cis is used to generate chunk- specific gff3: gffprocess uses external sort/grep/tabix to unify the chunks into a single tabix- indexed gff3 - pifdr() has been changed to avoid approximation on a grid and to compute binning of permuted scores more rapidly using hist(); old behavior recoverable with legacy=TRUE - ciseqByCluster() uses nested concurrency to perform cis searches gmapR ----- Changes in version 1.6.0: NEW FEATURES - Add median distance from nearest end (MDFNE) statistics to output of variantSummary. - Updated GSNAP, which is orders of magnitude faster than the previous version, brings many fixes and offers many new features. One new feature is the clip_overlap argument, which clips overlapping ends of read pairs (important for variant calling). - Updated bam_tally, which is faster and includes support for counting in soft-clipped regions. USER-VISIBLE CHANGES - Changes to tallyVariant statistics: drop the unique read position counts; renamed count.pos/count.neg to count.plus/count.minus (way better names) - tallyVariants does a better job of carrying over the Seqinfo from the BAM file. GOSemSim -------- Changes in version 1.21.3: - fixed minor bug in combineMethods <2013-12-16, Mon> graphite -------- Changes in version 1.9.4 (2014-04-04): - Updated Biocarta, KEGG, NCI and Reactome data. - New databases: HumanCyc and Panther. Gviz ---- Changes in version 1.8.0: NEW FEATURES - The new HighlightTrack class to add a comon highlighting region for multiple tracks. - The new OverlayTrack class to merge the panels of multiple tracks into a single panel. - The reverseStrand display parameter lets you plot the data relative to the negative strand. - The just.label display parameter adds control to the placement of group labls in AnnotationTrack and GeneRegionTrack objects. - The box.legend display parameter to add a box around the legend in a DataTrack object. - extend.right and extend.left now also take relative expansion factors (as values between -1 and 1). - A new shape type fixedArrow for AnnotationTrack and GeneRegionTrack objects, and the arrowHeadWidth and arrowHeadMaxWidth parameters to better control the arrow shapes. - Display parameter schemes to persistently modify parameter settings. - The new featureAnnotation and groupAnnotation parameters to better control the feature and group labels in AnnotationTracks. - The new exonAnnotation and transcriptAnnotation parameters to better control the exon and transcript labels in GeneRegionTracks. - The new AlignmentsTrack class to visualized aligned NGS reads in a BAM file. BUG FIXES - A number of significant fixes. SIGNIFICANT USER-VISIBLE CHANGES - Some display parameter names have been reworked, but the old ones should still work as aliases. - Overplotting in AnnotationTrack and GeneRegionTrack objects has been minimized to be able to make better use of alpha blending. Also the way composite exons (e.g. part UTR, part CDS) are plotted has been changed. Those will now be merged into one feature as long as the exon identifier is identical and if they can be reduced into a single range wit min.gapwidth=1. gwascat ------- Changes in version 1.7.6: USER VISIBLE CHANGES - bindcadd_snv has been added to bind CADD scores of Kircher et al. 2014 for SNVs to any GRanges query Changes in version 1.7.1: USER VISIBLE CHANGES - gwrngs is now serialized and explicitly made available in global workspace on attachment - gwcat data.frame is not generated on attachment CHANGES PRIOR TO VERSION 1.7.1 - May 30 2012 -- improve makeCurrentGwascat to handle chrX and p.Value suitably GWASTools --------- Changes in version 1.9.9: - added block size support for GDS files stored with scan,snp dimensions - gdsSubset and gdsSubsetCheck now operate on the fastest dimension of the GDS file Changes in version 1.9.8: - updates/bug fixes to gdsSubset/gdsSubsetCheck - different missing value attributes may be set if sub.storage type is different. Changes in version 1.9.7: - Added gdsSubset and gdsSubsetCheck functions to make a subset GDS file that includes only specified SNPs and scans from an existing GDS file - Updated gdsImputedDosage and gdsCheckImputedDosage to account for IMPUTE2 gprobs files that have missing values (specified by three equal probability strings) - Updated gdsCheckImputedDosage to produce optional logfile reporting any missing genotypes Changes in version 1.9.6: - Revised anomFilterBAF - fewer centromere spanning anomalies that aren't real, corrects some merging issues (previously it would merge sections that really were different split widths). Users should be aware that this will increase running time. Changes in version 1.9.5: - Remove defunct functions. - Improve efficiency of gwasExactHW, mendelErr, assocTestRegression (reduce number of calls to rbind). Changes in version 1.9.4: - Bug fix in getChromosome method for SnpAnnotationDataFrame (proper behavior of unnamed "index" argument). Changes in version 1.9.3: - Added gdsImputedDosage function. - GdsGenotypeReader can return transposed genotypes. Changes in version 1.9.2: - ScanAnnotationDataFrame and ScanAnnotationSQLite allow non-integer scanID. - Fix getAlleleA and getAlleleB in GdsGenotypeReader to work with indels. Changes in version 1.9.1: - Documentation now located in vignettes/ folder. - Added ibdAssignRelationshipsKing. - Added support for genotype GDS files with scan x snp dimensions in GdsGenotypeReader. HiTC ---- Changes in version 1.7.11: NEW FEATURES - Update NAMESPACE for BioC 2.14 BUG FIXES - Fix a bug in the getRestrictionSitesPerChromosome and matchPattern function (fixed=TRUE). If FALSE, all 'N' are reported. Changes in version 1.7.5: NEW FEATURES - Update for BioC 2.14 SIGNIFICANT USER-VISIBLE CHANGES - Add fit.out parameter in the plotIntraDist to remove the outliers during the regression Changes in version 1.7.4: SIGNIFICANT USER-VISIBLE CHANGES - New parameter for normICE - spars.filter, to filter out the more sparse bins before normlization - Change the parameters of getAnnotatedRestrictionSites and setGenomicFeatures functions - Update of the setGenomicAnnotation function to fit with the original HiCNorm method BUG FIXES - isSymmetrix - NA values - Bug in definition of upstream and downstream flanking region for a restriction site in getAnnotatedRestrictionSites Changes in version 1.7.3: NEW FEATURES - Add new normalization method for Hi-C data from Hu et al (HiCNorm). This method is based on linear regression model between interaction counts and sources of bias such as GC content, mappability, fragment length, etc. See normLGF(), setGenomicFeatures(), getAnnotatedRestrictionSites(). - Add new normalization method for Hi-C data from Imakaev et al.(ICE). The ICE procedure is an iterative normalization method used to remove any bias from HiC data. - Add 'summary' method for HTCexp and HTClist objects SIGNIFICANT USER-VISIBLE CHANGES - Improve quality control methods based using sparse data - Change method option for normPerTrans methods. The 'mean' method is in fact a 'max' method - Update of the export.my5C list format BUG FIXES - max (na.rm=TRUE) in mapC function HTSeqGenie ---------- Changes in version 3.13.13: - removed the "no job lefts" tests in test.sclapply() Changes in version 3.13.12: - now uses TP53Which() (instead of which.rds) for variant calling tests - now builds in BioC Changes in version 3.13.11: - now use TxDb.Hsapiens.UCSC.hg19.knownGene's version number in the TP53 genomic feature cache file, to avoid bugs when updating TxDb.Hsapiens.UCSC.hg19.knownGene Changes in version 3.13.10: - added an optional which config to limit VariantTools variant calling to certain regions Changes in version 3.13.9: - NA Changes in version 3.13.8: - fixed the "as.vector(x, mode) : invalid 'mode' argument" bug by adding the "importFrom(BiocGenerics,table)" NAMESPACE directive Changes in version 3.13.7: - enable indelRealigner in runPipeline controlled by config value of alignReads.do Changes in version 3.13.6: - set gatk.path in options if GATK_PATH env is set to an existing file. This is mostly for allowing the unit tests to know if and where a GATK is installed Changes in version 3.13.5: - require bamtally bugfixed version of gmapR Changes in version 3.13.4: - fixed bug in generateCountFeaturesPlots() when no genes left after filtering. Practically only happens for bacterial or viral genomes when every gene is hit more than 200 times Changes in version 3.13.3: - now saving fragmentLength in summary_coverage.txt - using Jinfeng's weighted mean to estimate fragmentLength - removed the parallelization in saveCoverage (since saveCoverage is used in parallel) Changes in version 3.13.2: - activate read trimming for illumina 1.5 quality using the 'B' as qual indicator Changes in version 3.13.1: - deactived the unit tests (test.wrap.callVariants, test.wrap.callVariants.parallel, test.wrap.callVariants.rmsk_dbsnp) until VariantAnnotation is fixed, to be able to compile HTSeqGenie on BioC servers Changes in version 3.13.0: - change to new dev cycle version number HTSFilter --------- Changes in version 1.2.1: - -- Minor bug fix for integeration in DESeq2 pipeline (which now has automatic independent filtering available) -- HTSFilter now accepts data with multi-factor designs for all input types illuminaio ---------- Changes in version 0.6.0 (2014-04-11): - The version number was bumped for the Bioconductor release version, which is now BioC v2.14 for R (>= 3.1.0). Changes in version 0.5.6 (2014-03-10): - Added a CITATION file, cf. citation("illuminaio"). Changes in version 0.5.5 (2014-01-19): - Added support for encrypted IDAT files where not all data fields are of the same length e.g. HumanHap550 v1. Changes in version 0.5.2 (2013-11-05): - moved testData to IlluminaDataTestFiles. - Added unitTests for encrypted IDATs. Changes in version 0.5.1 (2013-11-04): - Resshuffled internal code in readIDAT_nonenc so that seek() is always forward based. Changes in version 0.5.0: - The version number was bumped for the Bioconductor devel version. - No updates. inSilicoDb ---------- Changes in version 2.0.0: NEW FEATURES - Ability to access InSilico MySafe - New methods make it now possible to check the accessibility of data - Better integration of curated data - Possibility to use SCAN and UPC normalizations OTHER - Changes in the API, check the documentation for more information inSilicoMerging --------------- Changes in version 1.8.0: NEW FEATURES - Possibility to use named lists instead of eSets, check the merge- method documentation for an example BUG FIXES - Measurements are now always sorted in the same order in phenoData and exprs OTHER - Previous "NONE" method only available when not specifying a batch effect removal method or by specifying NULL. intansv ------- Changes in version 1.2.1: Notes - Add support to SV prediction programs Lumpy and softSearch. - Modify methodsMerge to make it more robust. - Modify all the read functions to coordinate methodsMerge. isobar ------ Changes in version 1.9.3: - allow the use of a combination matrix in NoiseModel reporterTagNames - added function getProteinInfoFromTheInternet which automatically recognizes Uniprot and Entrez ACs. Set now as default 'protein.info.f' in the report configuration. - Overhauled isobar-analysis.Rnw - use of ltxtables to allow optimal column widths (longer runtime, however) - use [[ instead of $ for accession of lists - better column and grouping description - allow report generation without a proteinInfo object - set report cache directory to 'cache' (instead of '.') by default - 1.9.3.2: - mascotParser2.pl: allow to skip modif-conversion with -no-modiconv - mascotParser2.pl: set --lightXML as default - report generation: set combn.method="versus.channel", which computes the ratios against the first channel - various PDF report improvements - 1.9.3.3: - report tables are written into tables which are loaded with LTxtable report generation takes longer now - fixes in correct.peptide.ratios - use combined protein group for peptide-protein mapping - use only reporter proteins for mapping - fix in creation of protein groups from template, subset by peptide _and_ modif Changes in version 1.9.2: - fix issue of NA in 'n.spectra' when calculating summarized ratios - various report improvements: - use column of variable width to display class labels - add attributes of quant table to summarized result table - improved placement of tikz peptide group pictures KEGGgraph --------- Changes in version 1.21.1 (2013-10-17): BUG FIXES - mergeKEGGgraph can handle NULL objects now - KEGGpathway2Graph eliminates duplicated edges so that parseKGML2DataFrame does not fail. (Thanks to Paul Shannon's bug report) - Paul Shannon added a set of RUnit tests to KEGGgraph limma ----- Changes in version 3.20.0: - New functions diffSplice(), topSplice() and plotSplice() provide functionality to analyse differential splicing using exon-level expression data from either microarrays or RNA-seq. - New Pasilla case study added to User's Guide, demonstrating differential splicing analysis of RNA-seq data. - new function weightedLowess() which fits a lowess curve with prior weights. Unlike previous implementations of lowess or loess, the weights are used in calculating which neighbouring points to include in each local regression as well as in the local regression itself. - weightedLoess() now becomes the default method used by loessFit() to fit the loess curve when there are weights. The previous locfit and loess() methods are offered as options. - linear model fit functions lm.series(), mrlm.series() and gls.series() no longer drop the dimensions of the components of the fitted object when there is just coefficient or just one gene. Previously this was done inconsistently in some cases but not others. Now the matrix components always keep dimensions. - The functions lmFit(), eBayes() and tmixture.vector() now work even when there is just one gene (one row of data). - New function subsetListOfArrays(), which is used to simplify the subsetting code for RGList, MAList, EList, EListRaw and MArrayLM objects. - new function tricubeMovingAverage() for smoothing a time series. - barcodeplot() has a new option to add enrichment worms to the plot, making use of tricubeMovingAverage(). - New plot() methods for RGList, MAList, EList and MArrayLM class objects. In each case, this produces a similar result to plotMA(). When using plot() or plotMA() on an MArrayLM object, the column is now specified by the 'coef' argument instead of by 'array'. - plotMA3by2() now works on single channel data objects as well as on MAList objects. - New function read.idat() to read files from Illumina expression beadarrays in IDAT format. - The ctrlpath argument of read.ilmn() now defaults to the same as path for regular probes. This means that only one path setting is required if the regular and control probe profiles are in the same directory. - read.ilmn() now sets the same probe IDs as rownames for both the expression matrix E and the annotation data.frame genes, providing that the probe IDs are unique. - beadCountWeights() can now work with either probe-wise standard errors or probe-wise standard deviations. - treat() has new arguments robust and winsor.tail.p which are passed through to robust empirical Bayes estimation. - topTreat() now includes ... argument which is passed to topTable(). - topTable() with confint=TRUE now produces confidence intervals based on the t-distribution instead of on the normal distribution. It also now accepts a numeric value for the confint argument to specify a confidence level other the default of 0.95. - topTable() will now work on an MArrayLM fit object that is missing the lods component, for example as produced by treat(). - roast() and mroast() now permit array weights and observation weights to both be specified. - camera(), roast() and mroast() now use getEAWP() to interpret the data object. This means that they now work on any class of data object that lmFit() will. - romer() now uses propTrueNull(method="lfdr") instead of convest(). This makes it substantially faster when the number of genes is large. - genas() now uses fit$df.total from the MArrayLM object. This prevents df.total from exceeding the total pooled residual df for the dataset. The genas() results will change slightly for datasets for which df.prior was very lage. - plotDensities() is now an S3 generic function with methods for RGList, MAList, EListRaw and EList objects. - plotFB is now an S3 generic function with methods for RGList and EList data objects. - New topic help pages 10GeneSetTests.Rd and 11RNAseq.Rd. The page 10Other.Rd is deleted. All topic help pages are now listed under 'See also' in the package introduction page accessible by ?limma. - avereps() was never intended to be applied to RGList or EListRaw objects. It now gives an error when applied to these objects instead of returning a matrix of questionable value. - Bug fix: fitFDistRobustly() was failing when there were missing values or zero df values and covariate was NULL. - Bug fix: vennDiagram() wasn't passing extra arguments (...) to plot() when the number of sets was greater than 3. - Bug fix to topTreat(). Rownames were incorrectly ordered when p<1. - bug fix to genas(), which was not handling vector df.prior correctly when the fit object was generated using robust=TRUE. - bug fix to squeezeVar(). Previously there was an error when robust=TRUE and trend=FALSE and some of the estimated df.prior were infinite. - bug fix to topTable() and topTableF() when sorting by F-statistic combined with p-value or lfc cutoffs. metagenomeSeq ------------- Changes in version 1.5 (2014-04-17): - Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function. - Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions. - Renamed MRfisher to fitPA (presence-absence fisher test). - Added warnings for normalization - Added fitDO (Discovery odds ratio test) and fitMeta (original metastats). - Added match.call() info to fitZig output - Fixed missing E-Step bounds metaMS ------ Changes in version 0.99.8: - fixed documentation for previous fix... Changes in version 0.99.7: - fixed incomplete GC settings Changes in version 0.99.6: - replaced paste(..., "/") with file.path() in runLC.Rnw metaseqR -------- Changes in version 1.0.0 (2014-04-11): NEW FEATURES - Function to calculate the F1-score (or harmonic mean of precision and recall) - Mature and tested enough to go from 0.x.y version to 1.0.0 Changes in version 0.99.6 (2014-04-09): NEW FEATURES - Example on how to estimate statistical test weights in the vignette BUG FIXES - Bug when exporting flags when gene or exon filters are NULL Changes in version 0.99.5 (2014-03-31): NEW FEATURES - Changed directory structure of the report to look more organized and pro - Added the ability to save and retrieve the gene model counts list (counts for each exon) in an .RData file to be reused in another analysis later, as summarizing genes is one of the most time-consuming parts. BUG FIXES - Minor problems with the report Changes in version 0.99.4 (2014-03-18): BUG FIXES - Removed all <<- assignments - Changed the Depends of DESCRIPTION file to import less packages in the main environment - Added qvalue package to Depends as there was a problem with NBPSeq Changes in version 0.99.3 (2014-03-17): NEW FEATURES - Function to check and warn if a main metaseqr argument is invalid (may prevent crashes during run) BUG FIXES - Small bug fix in read2count function Changes in version 0.99.2 (2014-03-14): NEW FEATURES - Ability to display only the top x% of significant genes to avoid excessively big reports BUG FIXES - More code and codestyle changes to comply with Bioconductor's guidelines Changes in version 0.99.1 (2014-03-12): NEW FEATURES - Ability to export counts table (raw and normalized) when reading from BAM files or just normalized otherwise - Valid examples for many functions BUG FIXES - More code and codestyle changes to comply with Bioconductor's guidelines Changes in version 0.99.0 (2014-02-21): NEW FEATURES - Support for Pan troglodytes - Improved the simulator to i) simulate length bias and ii) better length selection BUG FIXES - Code changes to comply with Bioconductor's guidelines Changes in version 0.93.0 (2014-02-12): NEW FEATURES - Support for Arabidopsis thaliana - Additional validation functions BUG FIXES - Bugs affecting multilevel factorial analysis (single factor, more than two conditions) - Smaller bug fixes Changes in version 0.92.0 (2014-01-25): NEW FEATURES - Functions to estimate weights for combining p-values based on simulated datasets from real data BUG FIXES - Smaller bug fixes Changes in version 0.91.0 (2014-01-03): NEW FEATURES - Functions to create simulated datasets - Functions to create false discovery and ROC curves BUG FIXES - A bug in p-value vector naming causing unordered p-values for limma and baySeq when combining methods - Smaller bug fixes Changes in version 0.9.1 (2013-11-27): NEW FEATURES - Permutation methods for combining p-values from multiple statistics - More interactive and compact report BUG FIXES - A bug in exon filters resulting in removing genes/transcripts with only one exon - A serious bug in exon filters causing wrong genes to be filtered out under circumstances Changes in version 0.9.0 (2013-11-21): NEW FEATURES - First release MIMOSA ------ Changes in version 0.99.2: - Added unit tests - Passing BiocCheck - Remove dependency on `multicore`. Now `parallel` only. Changes in version 0.9.12: - MIMOSA now returns a MIMOSAResultList S3 class. A lightweight wrapper for a list, with methods defined to extract the `fdr` and `pData`, `getW`, and `getZ` to extract the component weights and posterior probabilities, respectively. - `print` for `MIMOSAResult` and `MIMOSAResultList` - extractors for `countsTable`, the table of counts used to fit the model. Takes an argument to return the proportions or the counts. - MIMOSA checks throws a more informative warning if the data is filtered into oblivion when not properly paired (e.g. when the user doesn't aggregate over replicate negative controls, for example. ) - `volcanoPlot` implemented for MIMOSAResultList - Cleaned up package warnings and notes. - Cleaned up imports and depends. Changes in version 0.9.9: - Bug Fixes ** Filtered out empty categories on the conditioning variables. ** Support for parallel as well as multicore - News ** multicore support (via the multicore package) will be phased out in favor of the parallel package. Changes in version 0.8.0: - Model fitting via the 'MIMOSA' function - Data represented via an ExpressionSet - Formula interface support - Removed old code, including ICS class, and dependencies upon it. - New documentation Changes in version 0.7.0: - First beta release of MIMOSA - model fitting via MCMC through the .fitMCMC function minfi ----- Changes in version 1.9: - Importing the changes from 1.8 into 1.9. - Added the withColor argument to the getProbeType function, which allows the return of "IGrn", "IRed", "II", instead of only "I", "II". - Added asList argument to getControlAddress to return result as a list. - Moved reshape from Depends to Imports. - Dramatic improvement in memory usage of preprocessRaw. - Updated CITATION, the minif paper is in press. - Fixed bug with mapToGenome(..., mergeManifest = TRUE) reported by Dale Watkins <dale.watkins at="" sahmri.com=""> and Allegra A. Petti <apetti at="" genome.wustl.edu="">. - Fixed bug with mapToGenome(rSet) with rSet being a RatioSet with the CN set to NULL reported byAllegra A. Petti <apetti at="" genome.wustl.edu="">. - Added preprocessFunnorm, a new preprocessing method. - Improvements to the speed of getAnnotation by Martin Morgan <mtmorgan at="" fhcrc.org="">. MotifDb ------- Changes in version 1.5.9: NEW FEATURES - JASPAR_2014 added, with 592 motifs motifStack ---------- Changes in version 1.7.7: NEW FEATURES - No changes classified as 'new features' (package under active development) - add ic.scale parameter to plotMotifLogo. BUG FIXES - Fix bugs for motifSignature when the distance is larger than maximal distance. - No changes classified as 'bug fixes' (package under active development) Changes in version 1.7.6: NEW FEATURES - Change the class of signature to include the color sets. BUG FIXES - Allow motifSignature to accept Non-Binary Trees. Changes in version 1.7.5: NEW FEATURES - Change the output of motifStack for further steps. BUG FIXES - No changes classified as 'bug fixes' (package under active development) Changes in version 1.7.3: NEW FEATURES - Change the output of readPCM from a matrix to a list of pcm objects. BUG FIXES - No changes classified as 'bug fixes' (package under active development) Changes in version 1.7.2: NEW FEATURES - No changes classified as 'new features' (package under active development) BUG FIXES - fix the bugs of changing plot layout when using plotMotifLogoStackWithTree Changes in version 1.7.1: NEW FEATURES - No changes classified as 'new features' (package under active development) BUG FIXES - fix the bugs of leave names and plot region MSnbase ------- Changes in version 1.11.14: - update dependency to R >= 3.1 [2014-04-05 Sat] Changes in version 1.11.13: - Document [get|grep]Ecols in io vignette [2014-03-31 Mon] - typo in readMSnSet man [2014-03-31 Mon] - updated affiliation in vignettes [2014-03-31 Mon] Changes in version 1.11.12: - Fixed a bug in readMzTabData reported by Hendrik Weisser [2014-03-26 Wed] Changes in version 1.11.11: - precomputed msx test data now has id data [2014-03-25 Tue] - quantitation unit tests [2014-03-25 Tue] - quantify method now accepts label-free methods [2014-03-25 Tue] Changes in version 1.11.10: - import mzID [2014-03-20 Thu] - dummyiTRAQ id extdata [2014-03-21 Fri] - add addIdentificationData method for MSnExp and MSnSet [2014-03-21 Fri] - using data from pRolocdata (was pRoloc) [2014-03-23 Sun] - added removeNoId,MSnExp,MSnSet methods [2014-03-23 Sun] - added idSummary,MSnExp,MSnSet methods [2014-03-24 Mon] - Not generating different sample per file when reading raw data. pData(.) now has systematically 1 row if not specifically provided by the user. A message is also reported by validity,pSet if row(pData(.)) > 1. [2014-03-24 Mon] - NAnnotatedDataFrame now has default multiplex 1 [2014-03-25 Tue] - NAnnotatedDataFrame unit tests [2014-03-25 Tue] Changes in version 1.11.9: - write.exprs can have fDataCol or fcol (for consistence) [2014-03-17 Mon] - Fixing bug in combineFeatures(..., is.character(groupBy)) [2014-03-19 Wed] - fixed combineFeatures [2014-03-20 Thu] - added example, test and doc for combineFeatures with list [2014-03-20 Thu] Changes in version 1.11.8: - adding redundancy handling to combineFeatures (by vladpetyuk, pull request #18) [2014-03-14 Fri] - updated combineFeatures signature to accomodate above changes [2014-03-14 Fri] - updated unit tests for new testhat 0.8 [2014-03-14 Fri] Changes in version 1.11.7: - NA Changes in version 1.11.6: - add corresponding xcms functions to the chromatogram and xic manual page [2014-02-21 Fri] - new bpca imputation methods [2014-02-27 Thu] - replacing stop_on_error with option in vignette [2014-02-27 Thu] Changes in version 1.11.5: - typo in MSnSet droplevels man [2014-01-27 Mon] - typo in MSnbase-demo vignette [2014-02-20 Thu] - fix BPI legend in chromatogram [2014-02-20 Thu] Changes in version 1.11.4: - passing ... to sweep when normalising [2013-12-08 Sun] - updated makeMTD to accomodate new MS ontology [2013-12-23 Mon] Changes in version 1.11.3: - updated mzTab example files to new url [2013-11-15 Fri] - warning about mzTab versions [2013-11-15 Fri] Changes in version 1.11.2: - move inst/doc to vignettes [2013-10-19 Sat] Changes in version 1.11.1: - document na.rm in combineFeatures Rd [2013-10-18 Fri] Changes in version 1.11.0: - New devel version for Bioc 2.14 MSstats ------- Changes in version 2.1.3: - fix the groupComparison for label-free experiments. - automatically generate progress report as .txt files - add progress message for groupComparison and dataProcessPlots function. Changes in version 2.1.1: - fix the bug in Condition plot : 1. for label-based : match reference and endogenous 2. for label-free : when there is one observation in each group, SD=NA. make it zero. - fix the bug in heatmap and comparison plots : remove NA result for plotting - fix the bug for label-free groupComparison : how to get subject_nested parameter in make.contrast.free for unequal number per group - fix the bug in group quantification : make.contrast.group.quantification fixed for subject_nested parameter mzID ---- Changes in version 1.1.6: - Added documentation Changes in version 1.1.5: - Now computes mzR compatible acquisitionNum for the scans (thanks to Sebastian Gibb) - Checks for existence of local files (thanks to Sebastian Gibb) - XML moved from depend to import Changes in version 1.1.4: - Now computes mzR compatible acquisitionNum for the scans (thanks to Sebastion Gibb) - Various bug fixes Changes in version 1.1.3: - Introducing the mzIDCollection class to handle multiple mzID objects Changes in version 1.1.2: - Added the possibility to create the different 'sub'classes of mzID directly from a file without first having an internal xml representation and namespace Changes in version 1.1.1: - Fixed bug where multiple names in the modification rules would crash the parsing. Multiple names gets collapsed with '/' mzR --- Changes in version 1.9.8: - Pointing to the relevant wiki page in the Rcpp compiler/linker warning [2014-04-03 Thu] Changes in version 1.9.7: - modify to new biocViews to DESCRIPTION file (s.arora) Changes in version 1.9.6: - import all of Rcpp to avoid warnings in reverse dependencies <2014-02-14 Fri> Changes in version 1.9.3: - fix a string in ramp.cpp to enable compilation on clang-3.4 Changes in version 1.9.2: - version bump for Rcpp 0.10.6 <2013-10-30 Wed> Changes in version 1.9.1: - moved vignettes to /vignettes <2013-10-17 Thu> nondetects ---------- Changes in version 0.99.2: BUG FIXES - Added informative NEWS file. - Added version information to DESCRIPTION file. Changes in version 0.99.1: BUG FIXES - Changes in coding style to make package consistent with Bioconductor. - New biocViews added to package. - Added importing of pData from Biobase package. - Added unit tests. Changes in version 0.99.0: - Package released. npGSEA ------ Changes in version 0.99.0: - Package submitted to Bioconductor (March 31 2014) pathview -------- Changes in version 1.3.6: - ajusted node x coordinate by +0.5 to better fit the color blocks in 2 layer native kegg views. Changes in version 1.3.4: - updated bods to included an extra column of id.type, the default gene ID type. Changes in version 1.2.4: - updated korg to included over 600 newly added species. Pathview can work with 2970 species now. - Make returned values from pathview, keggview.native and keggview.graph functions invisible. Changes in version 1.2.3: - Fixed bug in node.map function, which produces 0 values when all multiple genes in a node are NA's. Changes in version 1.2.2: - Fixed bug in mol.sum function, which generates "incorrect number of dimension" or NA's when sum.method="median" etc. Changes in version 1.2.1: - Fixed bug in "missing red disease gene node labels" in diease pathways. To avoid interfering with node coloring, set all disease gene labels to black instead. phyloseq -------- Changes in version 1.7.24: USER-VISIBLE CHANGES - Added support for [Partial] Constrained Analysis of Principal Coordinates (CAP). - A supported/documented option in `ordinate`, supported by `plot_ordination`. - This solves [Issue 312](https://github.com/joey711/phyloseq/issues/312). - The `ordinate` function now takes an explicit `formula` argument. - This facilitates reliable contrained ordination calls for: - CAP (this commit) - RDA (partial redundancy analysis) - CCA (constrained correspondence analysis) Changes in version 1.7.23: USER-VISIBLE CHANGES - Refactor `plot_ordination` to be more stable, error less and give informative warnings. - Expect no critical API changes. Some errors now informative warnings with useful auto-changes to parameters. - The `type='biplot'` option no longer hard-specifies a discrete color scale. Available default pallette should work. - For `type='biplot'`, the non-variable (Taxa or Sample) label will always appear first in a discrete legend. Changes in version 1.7.22: USER-VISIBLE CHANGES - Revised psmelt to automatically modify data column-name conflicts, with warning - Udpated `psmelt` doc to formally notify users of these potential conflicts. - This solves Issue 307: https://github.com/joey711/phyloseq/issues/307 Changes in version 1.7.21: USER-VISIBLE CHANGES - Updated `import_qiime` doc to emphasize it is intended for legacy QIIME files. - Much faster and mem-efficient import of legacy QIIME and usearch files. - Uses data.table syntax to better manage import of large files. - Entire HMPv35 now imports in about 1 minute, low risk of mem-swap. - Added dependency to data.table Changes in version 1.7.20: USER-VISIBLE CHANGES - No user-visible changes. All future compatibility changes. BUG FIXES - Unit test changes to work with upcoming R release and new testthat version. Changes in version 1.7.19: USER-VISIBLE CHANGES - Documentation revisions. Faster examples, updated links. Changes in version 1.7.18: USER-VISIBLE CHANGES - Fix minor bug that prohibited parallel execution of weighted UniFrac Changes in version 1.7.17: USER-VISIBLE CHANGES - Added `import_usearch_uc` Added first-time support for usearch ?.uc? style output table. Addresses Issue 286, importing from UPARSE. https://github.com/joey711/phyloseq/issues/286 Further feedback on performance, use-cases, should be posted there. Changes in version 1.7.16: USER-VISIBLE CHANGES - Fixed minor bug affecting legend-order in `plot_network` Issue 288, https://github.com/joey711/phyloseq/issues/288 Changes in version 1.7.15: USER-VISIBLE CHANGES - `tip_glom` now uses standard R clustering tools, and takes their arguments documentation and tests updated to reflect the change much simpler, faster - `merge_taxa` now uses abundance to determine the achetype by default. Previously arbitrary. Changes in version 1.7.14: USER-VISIBLE CHANGES - Minor change in mixture model vignette, revised graphic Changes in version 1.7.13: USER-VISIBLE CHANGES - Deprecated originalUniFrac() internal function old (original) unifrac algorithm no longer supported. Addresses Issue 66: https://github.com/joey711/phyloseq/issues/66 Changes in version 1.7.12: USER-VISIBLE CHANGES - Formal deprecation of functions using .Deprecated Issue 269, https://github.com/joey711/phyloseq/issues/269 - Fixed bug in interface with vegan::fisher.alpha(..., se=TRUE). vegan doc states that this returns a data.frame, but a data.frame is not returned in vegan version 1.7.10. phyloseq no checks output dimensions before processing in `estimate_richness` - Replaced deprecated functions in tests and documentation. Changes in version 1.7.11: USER-VISIBLE CHANGES - Adds warning in make_network() and error in plot_network if empty graph encountered Issue 275, check/warning for empty igraph objects https://github.com/joey711/phyloseq/issues/275 - rarefy_even_depth() messages changed from cat() to messages(), and optional verbose argument added https://github.com/joey711/phyloseq/issues/263 Changes in version 1.7.10: USER-VISIBLE CHANGES - Fixes build-error originating from change in ade4 NAMESPACE in version 1.6.2 - Change minimum ade4 version to 1.6.2 - Uncommented examples now included in documentation for DPCoA function Changes in version 1.7.9: USER-VISIBLE CHANGES - Fixed typo-derived bug in new vignette. - These changes allow user to build from source without error. Changes in version 1.7.8: USER-VISIBLE CHANGES - Package dependencies reduced/clarified: https://github.com/joey711/phyloseq/issues/259 Should reduce chances for collisions with other packages, and related issues. Removed any dependencies on the picante package. - Replaced picante::node.age() with a faster implementation, node_ages() Appears to be 3 times faster. Speeds up UniFrac() and tip_glom() calculations. Changes in version 1.7.7: USER-VISIBLE CHANGES - Tree fixes: https://github.com/joey711/phyloseq/issues/235 https://github.com/joey711/phyloseq/issues/255 - If a tree has NA branch-length values, they are automatically set to 0. This occurs within both phyloseq(), and read_tree(). - UniFrac calculations require a rooted tree. While a rooted tree is not required to be part of a phyloseq object, it is a helpful default behavior to select a random root when UniFrac is called and the tree is unrooted, flashing a notice to the user. - Precise import from ape-package, rather than full-import. Smaller chance for collisions. Precisely-defined dependencies listed in NAMESPACE - As a result of the previous, phyloseq defines a placeholder "phylo" class, extended from "list". This seems to match the class from a full import of ape, and is necessary since ape does not export the "phylo" class. Changes in version 1.7.6: USER-VISIBLE CHANGES - Merged branches 1.7.4 and 1.7.5 Changes in version 1.7.5: NEW FEATURES - User-specified axis ordering to plot_heatmap() - User-specified axis edges to plot_heatmap() - This addresses: [Issue 237](https://github.com/joey711/phyloseq/issues/237) [Issue 230](https://github.com/joey711/phyloseq/issues/230) USER-VISIBLE CHANGES - New arguments to plot_heatmap(): `taxa.order`, `sample.order`, `first.sample`, `first.taxa` Changes in version 1.7.4: NEW FEATURES - import_mothur now handles more formats - Added documentation to discourage .group/.list formats Changes in version 1.7.3: NEW FEATURES - Added phyloseq_to_deseq2() wrapper function and examples for computing multiple OTU tests using Negative Binomial model and GLM (DESeq2). USER-VISIBLE CHANGES - Also added new .Rmd vignette for using DESeq, with colorectal carcinoma data Changes in version 1.7.2: USER-VISIBLE CHANGES - Reformat NEWS (this) file. Changes in version 1.7.1: USER-VISIBLE CHANGES - Rmd/HTML-based vignettes. No more Rnw/Sweave/PDF - Updated installer piano ----- Changes in version 1.4.0: NEW FEATURES - Added argument plot to consensusHeatmap() so that drawing the heatmap can be suppressed but the corresponding numerical matrix can be saved. - Added argument cellnote to consensusHeatmap() so that the information inside each cell of the heatmap can be chosen to be either the consensus scores (as previously), the median p-values, the number of genes or empty. - Added a matrix nGenesMat to the output of consensusHeatmap() containing the same information as printed in the heatmap if argument cellnote="nGenes". - Added arguments columnnames, colorkey, colorgrad and cex to consensusHeatmap() for better control of the column labels, toggling of the colorkey, color selection and text size. - Introduced the new function GSAheatmap(), which is similar to consensusHeatmap() but for only a single gene set result (gsaRes object). BUG FIXES - Fixed a bug which for some settings of runGSA would not output number of up- and downregulated genes in the gene sets. DOCUMENTATION - Updated consensusHeatmap() man page according to new changes in the function. - Added man page for GSAheatmap(). plethy ------ Changes in version 1.1.3: NEW FEATURES - Added 'summaryMeasures' method. - Added experimental heatmap-like plotting functionality 'plethy:::mvtsplot' procoil ------- Changes in version 1.13.2: - cleared up package dependencies and namespace - reference to Bioconductor Git-SVN bridge - minor corrections to vignette pRoloc ------ Changes in version 1.3.19: - fixed error introduced with mclust 4.3 (that now returns the data in the Mclust output - see comment in pRoloc:::gmmOutliers for details) [2014-04-07 Mon] Changes in version 1.3.18: - getPredictions can take class-specific scores [2014-04-04 Fri] Changes in version 1.3.17: - fixed newly introduced bug (see 1.3.16) in pRoloc:::subsetAsDataFrame - thank you unit tests for saving me, again [2014-03-26 Wed] Changes in version 1.3.16: - pRoloc:::subsetAsDataFrame now preserved original sample/column names [2014-03-24 Mon] - fixed wrong message when using col and pch in plot2D [2014-03-25 Tue] Changes in version 1.3.15: - updated pRolocmarkers("mmus") [2014-03-21 Fri] - moved extdata/*csv to pRolocdata [2014-03-23 Sun] - using *csv from pRolocdata [2014-03-23 Sun] Changes in version 1.3.14: - deleted tab character [2014-03-15 Sat] - added support for GMM parametrisation to phenoDisco [2014-03-17 Mon] - message instead of warning when using colour and pch [2014-03-21 Fri] - remove 1 duplicated mouse marker [2014-03-21 Fri] Changes in version 1.3.13: - fixed a bug in addLegend [2014-03-14 Fri] - updated testing to testthat 0.8 [2014-03-14 Fri] - Fixing several warnings about symnbols being replaced upon pRoloc loading and note about usage of ::: [2014-03-15 Sat] Changes in version 1.3.12: - added phenoDisco2 for testing, allows choice of GMM parameters [2014-02-26 Wed] - removed duplicated fly markers [2014-02-28 Fri] - updated affiliations in vignettes [2014-03-10 Mon] Changes in version 1.3.11: - modify to new biocViews to DESCRIPTION file by s.arora [2014-03-04] Changes in version 1.3.10: - new phenoDisco ndims argument to use more than two two principal components as input for discovery analysis [2014-01-03 Mon] - fixed and updated phenoDisco logging [2014-02-03 Mon] - added support for parallel phenoDisco execution. See BPPARAM argument [2014-02-03 Mon] - fixed issues with using PD and ndims [2014-02-10 Mon] - fixed call to anyUnknown in PD code [2014-02-10 Mon] - checking if duplicated markers in addMarkers [2014-02-14 Fri] Changes in version 1.3.9: - bump to force rebuild for new Rcpp Changes in version 1.3.8: - Removed trailing space in mmus nucleus markers [2014-01-21 Tue] - using filterNA to remove features with missing values in plot2D [2014-01-21 Tue] - fixed plot2D/addLegend [2014-01-23 Thu] Changes in version 1.3.7: - fixed addLegend to use correct colours (order) [2014-01-20 Mon] - fix typo in addMarkers man [2014-01-20 Mon] - re-arranged stockpch so that interleave full and empty plotting character [2014-01-20 Mon] 0 Removed last stockcol (tomato), too cose to "#FF7F00" [2014-01-20 Mon] Changes in version 1.3.6: - updated human markers: keep new pd.markers phenotypes, validated by Lisa and remove singletons [2014-01-14 Tue] - first stockpch is noe 19 [2014-01-16 Thu] - plot2D(.., pch) now taken into account for labelled data [2014-01-16 Thu] - removed alpha plot2D argument [2014-01-17 Fri] - updated plot2D and addLegend function with support for more organelle groups than colours. The previous versions are available as plot2D_v1 and addLegend_v1. [2014-01-17 Fri] Changes in version 1.3.5: - pRoloc citation [2014-01-12 Sun] Changes in version 1.3.4: - new unknownSet function [2013-12-11 Wed] - updated vignettes to account for tan2009r1 changes [2013-12-16 Mon] Changes in version 1.3.3: - update citation in phenoDisco.Rd [2013-11-22 Fri] - typos in vignettes [2013-11-25 Mon] Changes in version 1.3.2: - new markers [2013-11-06 Wed] - markers in vinette [2013-11-15 Fri] - mouse markers [2013-11-18 Mon] Changes in version 1.3.1: - using combineFeatures(..., na.rm=TRUE) in lopims pipeine [2013-10-22 Tue] - corrected spelling errors in phenoDisco doc [2013-10-29 Tue] Changes in version 1.3.0: - next devel version fot Bioc 2.14 PWMEnrich --------- Changes in version 3.5: - After further testing revert back to PWMEnrich 2.x group P-value algorithm - Introduced group sorting by top motifs Changes in version 3.1.4: - New way of estimating P-value for groups of sequences. Note this will produce different P-values for groups of sequences than PWMEnrich 2.x ! QDNAseq ------- Changes in version 1.0.0 (2014-04-14): INITIAL RELEASE - initial release as part of Bioconductor 2.14 qpgraph ------- Changes in version 1.20: USER VISIBLE CHANGES - Functions qpRndHMGM() and qpSampleFromHMGM() which were defunct in the previous release, are now removed from the package. - The execution of function qpGetCliques() can be now interrupted with CTRL+C and should allow to process GUI events. - Function qpBoundary() with argument logscale.bdsize=TRUE now handles plotting of boundaries of size 0 by setting them to 1 (=log(1)=0) for plotting purposes only. NEW FEATURES - Function qpCItest() when assuming a mixed GMM returns the fraction of variance explained (partial eta-squared) as estimate. See manual page for further details. BUG FIXES - Several bugfixes related to the simulation of mixed GMMs and eQTL networks. QuasR ----- Changes in version 1.4.0: NEW FEATURES - new arguments mapqMin and mapqMaxm in qCount, qProfile, qMeth and qExportWig allow to select alignments based on mapping quality - qAlign gains checkOnly argument which allows checking for existing alignments without triggering new alignments in case of missing ones r3Cseq ------ Changes in version 1.9.2 (2013-11-11): - fixed the bugs in function getFragmentsPerWindow for "overlapping window" Changes in version 1.9.1 (2013-10-21): - added the yLim input parameter of plotInteractionsNearViewpoint - added the log2 cutoff ratio for the function plotInteractionsNearViewpoint - fixed the shift of interaction in the viewpoint chromosome found in the function getFragmentsPerWindow - fixed the missing input parameter for the function getBatchReadCountPerWindow - fixed the class of r3CseqInBatch RamiGO ------ Changes in version 1.9.5: - RamiGO is now using AmiGO v2 Visualize as the default web server. Changes in version 1.9.1: - added citation information. Please cite http://bioinformatics.oxfordjournals.org/content/29/5/666.full Rariant ------- Changes in version 1.0.0: - First stable release with Bioconductor 2.14 (2014-04) rBiopaxParser ------------- Changes in version 2.1.7: - BUGFIX: fixed setkey for parsed biopax models - BUGFIX: fixed possible uses of complete URLs for ids (e.g. in PathwayCommons) - BUGFIX: fixed parameter checking failing due to data.table version 1.9.2. This will be fixed anyways when data.table 1.9.3. is out. Changes in version 2.1.5: - BUGFIX: Fixed several bugs relating to the default BioPAX version parameter biopaxlevel. - The package requires R >= 3.0 due to data.table requiring Reshape2, requiring plyr, requiring Rcpp. :-( Changes in version 2.1.3: - BUGFIX: Switched from rep_len to rep in order to continue R<3.0 support. Changes in version 2.1.1: - Attention: This is a major update and might introduce backwards incompatibility to previously parsed data! - Speed issues in previous versions were common with huge databases like Reactome or PathwayCommons, and with search & replace operations in the internal data.frame. - The data.table package is now required and imported for rBiopaxParser. - The internal data model has been switched from data.frame to data.table to speed up working with the rBiopaxParser. - The "df" slot of the biopax object, a data.frame object, is gone. Use the "dt" slot, a data.table, to directly access to biopax data. - If you work with the "df" slot of the biopax object in your current code, you have to make yourself comfortable with using the data.table syntax! - All functions which return a subset of the internal data, return a data.table object now. - A long standing bug of deeply nested XML instances has been fixed. See http://permalink.gmane.org/gmane.science.biology.informatics.conduct or/48534 - The default parameter specifying the Biopax Level (usually called biopaxlevel) has been changed and defaults to 3 now. - Functions selectInstances, getInstanceProperty, getReferencedIDs, splitComplex, getInstanceClass and many others now acceps either a biopax object or a compatible internal data.table. Changes in version 1.3.3: - fixed download links. Added links for the NCI databases with fixed XML encoding ( see discussion at http://sourceforge.net/mailarchive/message.php?msg_id=30106560) - added TemplateReactionRegulation to be plotted in pathway2RegulatoryGraph - future versions will likely switch to data.table support to deal with huge BioPAX databases from Reactome et al RDAVIDWebService ---------------- Changes in version 1.1.4: BUG FIXED - `getFunctionalAnnotationChartFile` bug was fixed. Now threshold and count parameter works as supposed (Thanks to Ulrik Stervbo) Changes in version 1.1.3: MINOR CHANGES - Added again into the repository. Changes in version 1.1.2: CODE CHANGES - In setAs(from="data.frame", to="DAVIDFunctionalAnnotationChart") function PValue field force to numeric data type (thanks to Marc Carlson) NEW FEATURES - Apache Axis time out parameter modification set/getTimeOut - Apache Axis http protocol version parameter modification set/getHttpProtocolVersion DOCUMENTATION - Vignette Trouble shooting section added with apache axis parameter examples. Changes in version 1.1.1: DOCUMENTATION - CITATION file was included. - Minor updates to DAVIDWebService-class and DAVIDWebService-package man pages and Roxygen2 quotes, in order to include the article citation. - Vignette email parameter invocation corrected. CODE CHANGES - DAVIDWebService initialize email parameter order modification (email, ..., url) DEPENDENCY CHANGES - Category, GO.db, RBGL and rJava packages were moved to import. - NAMESPACE file updated accordingly. Changes in version 1.1.0: MINOR CHANGES - Bump y in version x.y.z to odd number in 2.14 devel ReactomePA ---------- Changes in version 1.7.2: - bug fixed for multi-organisms support <2013-12-09, Mon> RedeR ----- Changes in version 1.12.0: - Improved interactive layout algorithm. - User interface is simplified, some shortcuts have been added. - Final release cycle of deprecated functions moved to the addGraph/getGraph related methods. - Deprecated plugin builder methods have been removed. RefNet ------ Changes in version 1.0.0: NEW FEATURES - Two sets of interactions, retrieved automatically from the AnnotationHub, in addition to the many provided by PSICQUIC: - gerstein-2012: "Architecture of the human regulatory network derived from ENCODE data", Gerstein et al, pmid 22955619 - hypoxiaSignaling-2006: "Hypoxia signalling in cancer and approaches to enforce tumour regression", Pouyssgur et al, pmid 16724055 - These interactions have been expressed in the standard RefNet 19-column format for easy querying. - a.canonical - b.canonical - relation - bidirectional - detectionMethod - pmid - a.organism - b.organism - a.common - a.canonicalIdType - b.common - b.canonicalIdType - cellType - a.modification - a.cellularComponent - b.modification - b.cellularComponent - provider - comment ReQON ----- Changes in version 1.9.1: - Minor changes were made to the vignette. September 4, 2012 Our manuscript describing ReQON has been published in BMC Bioinformatics. Refer to this paper for further description of the ReQON algorithm and a comparison with other quality score recalibration algorithms. Please cite this paper if you use our package. Cabanski CR et al. (2012) ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. BMC Bioinformatics 13(221). doi:10.1186/1471-2105-13-221. Rgraphviz --------- Changes in version 2.7: - Fixed include statements in Graphviz code. rhdf5 ----- Changes in version 2.8.0: NEW FEATURES - New function h5version implemented. - New low level general library functions H5open, H5close, H5garbage_collect, H5get_libversion, and H5Dset_extent implemented. USER VISIBLE CHANGES - h5createDataset automatically uses chunking and compression. - Added a warning if chunk size is equal to dimensions for large compressed datasets. BUG FIXES - C-stack overflow when reading large fixed-length strings. - error in i/o with chunksize or blocksize parameters. - compiling errors due to missing int return value. roar ---- Changes in version 0.99.6: NEW FEATURES - No new features, just adopted the suggested format for the NEWS file BUG FIXES - No changes classified as 'bug fixes' rols ---- Changes in version 1.5.2: - pretty printing with strwrap(mtd[...]) in vignette and termMetadata S3 printing method for readable output (suggestion from Martin Morgan) [2014-02-18 Tue] - Using BiocStyle vignette [2014-02-18 Tue] Changes in version 1.5.1: - split go terms (PRO:...) instead of ids (PR:...) in vignette tgnqueryShow chunk <2013-10-19 Sat> Changes in version 1.5.0: - new devel for Bioc 2.14 rpx --- Changes in version 0.99.9: - In pxref, dealing with cases without any or pending publications [2014-04-01 Tue] Changes in version 0.99.8: - fix leftover issues from renaming package (d.tenenbaum) [2014-03-30 Sun] Changes in version 0.99.7: - renamed to rpx due to CRAN name clash [2014-03-28] Changes in version 0.99.6: - more typos in vignette [2014-03-12 Wed] Changes in version 0.99.5: - Suggestions, biocView and typos reported by Nate Hayden [2014-03-12 Wed] - added Runit test [2014-03-12 Wed] - use ae fonts in vignette [2014-03-12 Wed] Changes in version 0.99.4: - Update reference in man and vignette [2014-03-11 Tue] - Typos in vignette [2014-03-11 Tue] Changes in version 0.99.3: - reverting pxannounced to empty signature to fix warning [2014-03-05 Wed] Changes in version 0.99.2: - replacing download.file by getURL to download annoucement rss over https <2014-03-05 Wed> Changes in version 0.99.1: - fixing pxfiles ending by \r on Windows [2014-03-05 Wed] Changes in version 0.99.0: - added a vignette [2014-03-05 Wed] - handle invalid identifiers [2014-03-05 Wed] rqubic ------ Changes in version 1.8.1 (2011-08-02): - Fix errors in documentations Rsamtools --------- Changes in version 1.15.0: NEW FEATURES - asSam converts BAM files to SAM files - razip, bgzip re-compress directly from .gz files - yieldReduce through a BAM or other file, applying a MAP function to each chunk and reducing the result to it's final representation SIGNIFICANT USER-VISIBLE CHANGES - bgzip default extension changed to '.bgz' - seqinfo,BamFile-method attempts to return seqnames in 'natural' order, e.g., chr1, chr2, ... - yieldSize now works on BAM files queried with ranges. Successive ranges are input until the total number of records first equals or exceeds yieldSize.. - scanFa supports DNA, RNA, and AAStringSet return objects BUG FIXES - scanFa returns correct sequence at the very end of files - razip compresses small files - applyPileups no longer crashes in the absence of an index file Rsubread -------- Changes in version 1.14.0: NEW FEATURES - featureCounts automatically re-orders paired end reads if they were sorted by chromosomal locations in the input. It can also deal with read pairs in which only one end was included in the input. - featureCounts is more robust in processing different variants of GTF/GFF annotation files. - Subjunc can detect exon-exon junctions which are located at the start or end of reads. It can detect non-canonical junctions ('reportAllJunctions' option) in addition to canonical junctions, and it can also be used to detect chimerism in both RNA-seq and gDNA-seq data. - Both align (Subread aligner) and subjunc now take gzipped FASTQ files and outputs BAM files in their default settings. They accept multiple input files as well. - Breakpoint locations are reported along with mapping location of each fusion read in SAM/BAM files, using tags including CC(chromosome name), CP(mapping position), CG(CIGAR string) and CT(strand). - A full index (no gaps) can be built for a reference genome to further speed up read mapping. - qualityScores() and propmapped() functions were rewritten. - Bug fixes. rTANDEM ------- Changes in version 1.3.9: - Capitalisation aliases added for most functions. - The rtandem function now has an 'output.path' argument. BUG FIXES - Changed default parameters to prevent the risk of not generating output files. - Fixed a bug with 'rtandem()' where the function would not take a complex rTTAXO object as argument. Changes in version 1.3.8: BUG FIXES - Fixed a memory leak associated with PTMTreeSearch. - Removed an unwanted side-effect from the function GetPeptides(). Changes in version 1.3.7: NEW FEATURES - rTANDEM now includes the PTMTreeSearch scoring algorithm. - New function to set default values for PTMTreeSearch algorithm. Changes in version 1.3.5: NEW FEATURES - New rTResult_s class support saving spectra. - New function 'ms2.plot' to visualize spectra. Changes in version 1.3.4: NEW FEATURES - rTANDEM now supports TPP's hrk-score function. BUG FIXES - Fixed a bug with k-score function. Changes in version 1.3.3: NEW FEATURES - Functions have been implemented to create and manipulate parameter objects (S3 class rTParam). Those functions give default values for instrument-specific parameters for some types of mass spectrometer as well as default values for general parameters. Changes in version 1.3.2: NEW FEATURES - rTANDEM now supports the k-score function. It can be used by setting the parameter 'scoring, algorithm' to "k-score". RTN --- Changes in version 1.2.0: - Introduced variant set enrichment analysis for regulons. rTRM ---- Changes in version 1.2: - An arbitrary number of targets can be specified in findTRM(). This allows to use the same list of TFs for target and query, in order to identify TRMs using information from predicted TFBS only. - BioGRID dataset updated to release 3.2.11 (April 2014) - getBiogridData() retrieves by default the latest BioGRID release www.thebiogrid.org) SANTA ----- Changes in version 1.3.10 (2014-03-03): NOTES: - Fixed minor memory leak in the Knet function. sapFinder --------- Changes in version 0.99.4: BUG FIXES - *To fix a bug of "index.js" that may cause a confusing CSS layout of index html page. Changes in version 0.99.3: NEW FEATURES - *Add some BiocViews items to packages. *Reduce the size of testing data. *Make import and export much more continent. *To make package consistent with bioconductor in the coding style. *Use BiocStyle for vignette. BUG FIXES - *To fix a bug of vignette document that may cause the package checking to crash. Changes in version 0.99.2: BUG FIXES - *Resolve some errors and warnings. Changes in version 0.99.0: - *Package released. SCAN.UPC -------- Changes in version 2.5.8: NEW FEATURES - This package now provides "generic" functions for UPC normalizing any type of gene-expression data. These values can be input as vectors or ExpressionSet objects. This means that data from Illumina BeadChip microarrays or any other type of microarray can be UPC normalized with relative ease. It is also easy through integration with the GEOquery package to UPC normalize any preprocessed data set from GEO. - This package now uses the ComBat function from the sva package to make it easy to adjust gene expression data for batch effects. This can be done for any type of expression data. - RNA-Sequencing data can now be input as matrix files and/or where a header is present in the input data files. NOTES - The SCAN_TwoColor and UPC_TwoColor functions have changed. They now return ExpressionSet objects. - The SCAN_TwoColor and UPC_TwoColor methods now add an integer suffix to each probe for which there is a duplicate name. - The UPC_RNASeq function now also returns an ExpressionSet object. - A bug was fixed in which UPC_RNASeq returned NA values if there was no entry in the annotation file. SeqArray -------- Changes in version 1.3.2: - update test codes to avoid the conflict Changes in version 1.3.1: - update according to the new version of VariantAnnotation shinyTANDEM ----------- Changes in version 1.1.4: BUG FIXES - Better error handling, error messages and conditions for missing data. Changes in version 1.1.3: BUG FIXES - Corrected problems arising from incompatibility between data.table and data.frame subsetting syntaxes. Changes in version 1.1.2: NEW FEATURES - MS2 spectra can now be visualized. - The 'Result Statistics' and 'Peptides view' tab are now ready. BUG FIXES - Corrected a bug in the selection of proteins by number of peptides. ShortRead --------- Changes in version 1.21: NEW FEATURES - writeFastq can write (and does so by default) gz-compressed files SIGNIFICANT USER-VISIBLE CHANGES - Use BiocParallel rather than srapply, mark srapply as 'Deprecated' - qa,character-method defaults to type="fastq" - Input of 'legacy' formats marked as such - alphabetByCycle supports amino acid string sets snm --- Changes in version 1.11: - Now uses lme4 R (>= 1.0) - Default nbins=20 - New argument lmer.max.iter allows one to cap the number of lmer iterations SomaticSignatures ----------------- Changes in version 1.0.0: - First stable release with Bioconductor 2.14 (2014-04) supraHex -------- Changes in version 1.1.17: NEW FEATURES - Add new functions for advanced heatmap visualisation and tree-based analysis of sample relationships Changes in version 1.1.2: NEW FEATURES - Add a new function "sMapOverlay" to overlay additional data to the trained map synapter -------- Changes in version 1.5.7: - Enable setting number of missed cleavages (closes #53) [2014-03-24 Mon] Changes in version 1.5.6: - change the default value of grid.ppm.from to 2 (was 5 before) [2014-03-05 Wed] - change the separator in GridDetails' names to ":" (was "." before) [2014-03-07 Fri] - test for corresponding Pep3D file (closes #42) [2014-03-19 Wed] Changes in version 1.5.5: - fix a bug in the calculation of non unique matches in gridSearch2 (part of searchGrid); results in a higher number of non unique matches (some of the reported -2 will now be reported as 2 in the grid details) [2014-03-05 Wed] - partial rewrite of gridSearch2 (part of searchGrid) for faster grid calculation [2014-03-04 Tue] Changes in version 1.5.4: - biocViews update Changes in version 1.5.3: - modified findMSeEMRTs (part of searchGrid) for faster grid calculation [2014-02-28 Fri] - typos in manual [2014-02-25 Tue] - replace readFasta by Biostrings::readAAStringSet [2014-02-25 Tue] - replace digest by cleaver::cleave [2014-02-25 Tue] Changes in version 1.5.1: - typo in vignette [2014-02-18 Tue] Changes in version 1.5.0: - new devel version for Bioc 2.14 TargetSearch ------------ Changes in version 1.20.0: BUG FIXES - Write the actual retention index value instead of the work 'RI' in `ProfileCleanUp`. TCC --- Changes in version 1.3.2: - DESeq2 was implemented in TCC for identifying DEGs. - EBSeq was removed from TCC. - arguments of 'WAD' function were changed. - fixed bug in '.testByDeseq' that missing to treat size factors. - the strategies for DE analysis of paired two-group dataset were implemented. - add the section for describing DE analysis of paired two-group dataset into vignette. tigre ----- Changes in version 1.16.1: - More informative error messages TransView --------- Changes in version 1.7.4: BUG FIXES - Removed import error introduced with version 1.7.2 Changes in version 1.7.3: BUG FIXES - Minor bug fix Changes in version 1.7.2: NEW FEATURES - annotatePeaks now assigns a gene to the peak center instead of the peak limits - annotatePeaks takes the new argument 'reference' to enable alternative peak to gene body associations Changes in version 1.7.1: BUG FIXES - Minor correction to avoid warning messages issued after GRanges to data.frame conversion unifiedWMWqPCR -------------- Changes in version 0.9.9: SIGNIFICANT USER-VISIBLE CHANGES - First submission of uWMWqPCR to BioConductor. VariantAnnotation ----------------- Changes in version 1.10.0: NEW FEATURES - add support for ##contig in VCF header - add 'meta<-', 'info<-', 'geno<-' replacement methods for VCFHeader - add 'header<-' replacement method for VCF - add strand to output from locationVariants() - add support for writeVcf() to process Rle data in geno matrix - readVcf() now parses 'geno' fields with Number=G as ((#alleles + 1) * (#alleles + 2)) / 2 - writeVcf() now sorts the VCF when 'index=TRUE' - add 'fixed<-,VCFHeader,DataFrameList' method - add convenience functions for reading VCF into VRanges - add Rplinkseq test script - add 'isSNV', 'isInsertion', 'isDeletion', 'isIndel', 'isTransition', 'isPrecise', 'isSV' and 'isSubstitution' generics - add 'isSNV', 'isInsertion', 'isDeletion', 'isIndel' methods for VRanges and VCF classes - add match methods between ExpandedVCF and VRanges - add support for VRanges %in% TabixFile MODIFICATIONS - expand,VCF-method ignores 'AD' header of 'AD' geno is NULL - add support for SIFT.Hsapiens.dbSNP137 - remove locateVariants() dependence on chr7-sub.vcf.gz - modify expand() to handle 'AD' field where 'Number' is integer - rename readVRangesFromVCF() to readVcfAsVRanges() - remove check for circular chromosomes in locateVariants() and predictCoding() and refLocsToLocalLocs() - modify filterVcf() to handle ranges in ScanVcfParam - pass 'genetic.code' through predictCoding() - change default to 'row.names=TRUE' for readGT(), readGeno(), and readInfo() - fixed() on empty VCF now returns DataFrame with column names and data types vs an empty DataFrame - update biocViews - modify 'show,VCF' to represent empty values in XStringSet with '.' - replace rtracklayer:::pasteCollapse with unstrsplit() DEPRECATED and DEFUNCT - remove defunct dbSNPFilter(), regionfilter() and MatrixToSnpMatrix() - deprecate defunct readVcfLongForm() BUG FIXES - modify expand.geno() to handle case where header and geno don't match - modify writeVcf() to write out rownames with ":" character instead of treating as missing - fix how sample names were passed from 'ScanVcfParam' to scanVcf() - fix bug in 'show,VCF' method - fix bugs in VRanges -> VCF coercion methods - fix bug in lightweight read* functions that were ignoring samples in ScanVcfParam - fix bug in writeVcf() when no 'ALT' is present VariantFiltering ---------------- Changes in version 0.99: USER VISIBLE CHANGES - Submission of the first version to the Bioconductor project (start date: 26 September, 2013) VariantTools ------------ Changes in version 1.6.0: NEW FEATURES - Add pileupVariants function as an alternative to tallyVariants for computing nucleotide pileups using Rsamtools, instead of gmapR. In the future, this should allow VariantTools to become independent of gmapR, but the full variant statistics will only be available via tallyVariants. USER-VISIBLE CHANGES - See the NEWS for gmapR to learn about changes to tallyVariants output. wateRmelon ---------- 1.3.1: thanks to several users for bug reports! xcms ---- Changes in version 1.39.6: USER VISIBLE CHANGES - Massifquant reports the maximum intensity for each isotope trace (peak). This is useful for interactive parameter optimization. BUG FIXES - Major memory reduction in parallel fillPeaks() thanks to Jan Stanstrup. Now using an environment to mirror gvals to each list item in the very large argList. Changes in version 1.39.4: BUG FIXES - Fixed write.cdf(), which had an intensity offset of +1, added a unit test Changes in version 1.39.3: BUG FIXES - New R-devel check unload better. Lingering ramp code removed, import from mzR. Cleaned up other errors in package check. Changes in version 1.39.1: BUG FIXES - Updated doubleMatrix c code to allow for larger profile matrixes REQUIRED CHANGES - Moved inst/doc to vignettes yaqcaffy -------- Changes in version 1.23.1: - moved inst/doc to vignettes [2013-10-19 Sat] Packages removed from the release ================================= The following packages are no longer in the release: Agi4x44PreProcess, maDB, pgUtils