Showing : annotate • reset
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Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 22 months ago by ▴ 70 • written 23 months ago by ▴ 140
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 15 months ago by • 0 • written 2.0 years ago by • 0
4
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3
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 10
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
2.7 years ago Palmira • 0
1
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2
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3.5k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
2
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1
reply
837
views
The best pacakge to annotate a set of regions
annotate
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 20
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4
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1.8k
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Annotating a sequence, new to bioconductor
annotate
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
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3
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1.4k
views
How to annotate gene ontologies based on Gene Symbols in R
GO.db annotate
7.0 years ago dusan.petrovic • 0
0
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1
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1.5k
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RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
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4
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7.9k
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How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
oligo annotate
7.3 years ago llkxiaolan ▴ 10
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1
reply
2.9k
views
How many genes are appropriate for GO enrichment analysis
go annotate rna-seq clusterprofiler
updated 7.4 years ago by ▴ 120 • written 7.4 years ago by ▴ 20
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1.7k
views
querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 7.5 years ago by 4.1k • written 7.5 years ago by ▴ 50
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8
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2.1k
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Can't find Ly76 on my Affymetrix MoGene 2.0ST array annotated with pd.mogene.2.0.st package
pd.mogene.2.0.st mogene20sttranscriptcluster.db annotate
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
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3
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2.5k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 7.7 years ago by ▴ 370 • written 7.7 years ago by ▴ 10
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1
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1.5k
views
Annotation of Probe id to Gene
bioconductor annotate microarray arabidopsis thaliana
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
0
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4
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1.6k
views
TimmR error for hgu133a.db
software error annotate hgu133a
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
3
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6
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3.0k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
8.1 years ago MOD • 0
6
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5
replies
15k
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Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 10
1
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2
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2.5k
views
blastSequences queries failing due to BLAST switch to https?
annotate blastSequences BLAST https
updated 8.4 years ago by 25k • written 8.4 years ago by • 0
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2
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1.8k
views
Problems using intansv...
annotate annotate
updated 8.7 years ago by • 0 • written 10.9 years ago by ▴ 10
2
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1
reply
1.3k
views
Use matchPattern for large DNAStrings
biostrings annotate
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 40
0
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1
reply
1.7k
views
How to identify the microarray annotation library automatically from GEO study ID?
limma microarray annotation bioconductor annotate
updated 8.8 years ago by 68k • written 8.9 years ago by • 0
0
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1
reply
1.7k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 9.6 years ago by 16k • written 9.6 years ago by • 0
0
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1
reply
2.2k
views
Difference in TxDb.Hsapiens.UCSC.hg19.knownGene and UCSC knownGene
annotate exons txdb.hsapiens.ucsc.hg19.knowngene
9.7 years ago adnan.niazi • 0
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1
reply
1.5k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
10.2 years ago reuma • 0
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1
reply
1.9k
views
can't run functions in 'annotate'
annotate
10.3 years ago boris.steipe • 0
1
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2
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1.8k
views
about library(Homo.sapiens) from TxDb.Hsapiens.UCSC.hg18.knownGene
annotate
10.3 years ago Bogdan ▴ 670
2
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2
replies
2.1k
views
BLAST export library 'annotate'
blast annotate biostrings export fasta
10.3 years ago b.stielow • 0
5
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2
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11k
views
Probe to gene id conversion
annotate biomart probe to gene id
updated 10.4 years ago by 68k • written 10.4 years ago by ▴ 20
0
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6
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2.5k
views
Missing as.list generic from AnnotationDbi?
annotate AnnotationDbi annotate AnnotationDbi
updated 10.5 years ago by ★ 2.0k • written 11.7 years ago by ★ 7.9k
0
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2
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2.1k
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Bioconductor Digest, Vol 138, Issue 27
annotate biovizBase ggbio UniProt.ws Pbase annotate biovizBase ggbio UniProt.ws Pbase
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by 1.6k
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1
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1.7k
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Positional Details with Features through UniProt.ws Ultimately to display as tracks in ggbio
annotate ggbio annotate ggbio
updated 10.5 years ago by ▴ 490 • written 10.6 years ago by ▴ 30
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1.6k
views
ChIPpeakAnno
SNP Annotation annotate convert SNP Annotation annotate convert
10.6 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.5k
views
non-CpG methylated regions and strand information in MEDIPS output
BSgenome annotate biomaRt BSgenome MEDIPS BSgenome annotate biomaRt BSgenome MEDIPS
updated 10.6 years ago by ▴ 570 • written 10.6 years ago by ★ 13k
0
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1
reply
2.1k
views
annotation for TAqman assay IDs
Annotation probe annotate Annotation probe annotate
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 10
0
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2
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1.8k
views
Affymetrix mouse 430_2 array - annotation problem
Annotation mouse4302 annotate Annotation mouse4302 annotate
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 550
0
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5
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4.7k
views
annotating microarray data with mogene10stv1
Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 70
0
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2
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3.2k
views
Biomart annotation
annotate convert annotate convert
updated 10.7 years ago by ▴ 190 • written 10.7 years ago by ▴ 40
0
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5
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2.9k
views
Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 array probe sets
Annotation probe annotate annaffy oligo ReportingTools Annotation probe annotate annaffy
updated 10.7 years ago by ▴ 160 • written 10.8 years ago by 68k
1
vote
8
replies
4.2k
views
GRanges apply functions
GO annotate GO annotate
updated 10.7 years ago by ★ 4.2k • written 10.7 years ago by ▴ 380
0
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1
reply
3.9k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
10.8 years ago António Miguel de Jesus Domingues ▴ 510
0
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1
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1.8k
views
ChIPpeakAnno
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 10.9 years ago by ★ 4.3k • written 10.9 years ago by ▴ 350
0
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0
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1.2k
views
lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
annotate annotate
11.0 years ago Guest User ★ 13k
2
votes
1
reply
1.5k
views
HTqPCR- gene names not maintained in limmaCtData
annotate ddCt HTqPCR annotate ddCt HTqPCR
11.0 years ago Cornwell, Adam ▴ 110
0
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9
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2.3k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 11.1 years ago by 16k • written 11.1 years ago by ▴ 740
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0
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1.1k
views
Ontology
Annotation GO annotate GOstats Annotation GO annotate GOstats
11.1 years ago Marc Carlson ★ 7.2k
0
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0
replies
1.4k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
11.3 years ago Valerie Obenchain ★ 6.8k
0
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5
replies
1.7k
views
multiple annotations with get()?
Biobase annotate convert Biobase annotate convert
updated 11.4 years ago by 21k • written 11.4 years ago by ▴ 230
0
votes
2
replies
1.7k
views
limma_3.17.23 - missing ILMN identifiers in EList objects after read.ilmn
Annotation Normalization GO probe annotate Annotation Normalization GO probe annotate
updated 11.4 years ago by ★ 3.6k • written 11.4 years ago by ▴ 120
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Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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