Showing : Biostrings • reset
1
vote
4
replies
607
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 4 weeks ago by • 0
1
vote
3
replies
281
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 6 weeks ago by • 0
1
vote
1
reply
310
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
6 weeks ago Gerhard Thallinger ▴ 180
0
votes
2
replies
477
views
Is there a function that takes an amino acid string and returns all biologically possible substitutions?
Biostrings aminoacid motifbreakR
written 3 months ago by • 0
0
votes
1
reply
523
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 10 weeks ago by ▴ 60 • written 10 weeks ago by • 0
4
votes
2
replies
584
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 4 months ago by ▴ 180
2
votes
3
replies
1.4k
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
updated 6 months ago by 16k • written 6 months ago by • 0
3
votes
4
replies
576
views
Store output of matchPWM()
biostrings Biostrings
7 months ago • updated 6 months ago mat149 ▴ 80
0
votes
1
reply
389
views
Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 8 months ago by 67k • written 8 months ago by • 0
2
votes
2
replies
1.0k
views
From a DNAStringSet to a data.frame
Biostrings
8 months ago ramiro.barrantes ▴ 10
1
vote
5
replies
786
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
8 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
329
views
How to search for a string in a DNAStringSet dataset?
Biostrings
10 months ago Angela Michalichyn • 0
2
votes
6
replies
1.1k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 14 months ago by 16k • written 14 months ago by • 0
1
vote
3
replies
845
views
AAbin vs DNAbin structures
Biostrings
updated 14 months ago by 67k • written 14 months ago by • 0
0
votes
2
replies
967
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 19 months ago by ▴ 70
0
votes
0
replies
549
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
21 months ago Gilles • 0
0
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0
replies
689
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
22 months ago Mario Dejung • 0
0
votes
0
replies
848
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
23 months ago vonSkopnik • 0
0
votes
2
replies
961
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 6 weeks ago by ▴ 20 • written 23 months ago by • 0
0
votes
0
replies
812
views
how to get protein sequence similarity and gaps % using Biostrings
sequence-similarity gaps homology Biostrings pairwise-alignment
2.1 years ago biong • 0
0
votes
8
replies
1.6k
views
translate errors in fastq file reading
translate biostrings Biostrings
2.1 years ago Brett • 0
3
votes
5
replies
1.8k
views
Biostrings multiple pattern match
pattern Biostrings
updated 2.2 years ago by 16k • written 2.2 years ago by • 0
2
votes
2
replies
2.5k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.2 years ago Mog • 0
0
votes
1
reply
950
views
Using DNAStrings with Rcpp without converting to Character
Biostrings DNAString Rcpp
updated 2.3 years ago by 16k • written 2.6 years ago by • 0
0
votes
2
replies
1.8k
views
Subsetting a DNAStringSet object with many DNAString's
Biostrings
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 10
0
votes
1
reply
1.3k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
1
vote
0
replies
1.2k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.7 years ago L ▴ 50
0
votes
4
replies
2.4k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.7 years ago by 67k • written 2.7 years ago by • 0
0
votes
0
replies
835
views
How to make a pairwiseAlignment of circular sequences
Biostrings
2.8 years ago vonSkopnik • 0
5
votes
5
replies
1.8k
views
Changing genetic_code_table in Biostrings
Biostrings
2.8 years ago Sam • 0
0
votes
0
replies
614
views
Text display of entire `DNAMultipleAlignment` objects
Biostrings
2.8 years ago Charles Plessy ▴ 180
0
votes
0
replies
810
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.8 years ago Charles Plessy ▴ 180
0
votes
2
replies
986
views
Simple subject extraction question with biostrings
Biostrings
2.8 years ago James • 0
1
vote
6
replies
2.0k
views
DNAStringSet(x, start=, end=) loses quality information
Biostrings
updated 2.9 years ago by 16k • written 3.0 years ago by ▴ 180
1
vote
2
replies
1.6k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.0 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.1k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.0 years ago by 16k • written 3.0 years ago by • 0
1
vote
2
replies
1.2k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.0 years ago Madza Farias-Virgens • 0
0
votes
4
replies
3.7k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.3 years ago HELEN • 0
0
votes
0
replies
958
views
Bioconductor: Ambiguous Amino Acids & Gap Sequences
Translation Biostrings
3.3 years ago emmanuel.verde2939 • 0
4
votes
9
replies
2.0k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.5 years ago by 16k • written 3.5 years ago by ▴ 260
0
votes
0
replies
1.1k
views
matchPattern function for multiple patterns in R
matchPattern automatic Biostrings for-loop
3.7 years ago adklts • 0
0
votes
3
replies
1.2k
views
DESeq2 - extracting results - Gnomon gene model
DESeq2 Gnomon Biostrings
3.7 years ago sieminsk • 0
3
votes
2
replies
2.3k
views
Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
DNASeqData Biostrings
3.9 years ago • updated 3.8 years ago Benjamin ▴ 20
2
votes
3
replies
1.3k
views
Recycling a DNAStringSet over an IRangesList in extractAt()
Biostrings IRanges
4.0 years ago Nicholas Cooley • 0
6
votes
5
replies
2.0k
views
to extract the mRNA sequences of the canonical RefSeq genes
Biostrings
4.0 years ago Bogdan ▴ 670
1
vote
1
reply
959
views
Subset center regions of a set of different length sequences
Biostrings
updated 4.1 years ago by ▴ 10 • written 4.1 years ago by • 0
0
votes
0
replies
834
views
vcountPDict Out-of-Memory Errors
software error Biostrings
4.2 years ago JennyS • 0
0
votes
3
replies
1.9k
views
What is the use of the BStringSet?
BioStrings BStringSet StringSet
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
0
votes
4
replies
2.7k
views
Reverse translate from protein sequences into the most likely non-degenrate DNA coding sequence
biostrings
4.5 years ago moldach ▴ 20
1
vote
1
reply
1.0k
views
Heng Li's fastq parsing benchmark - attempt in R
biostrings gz
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 90
50 results • Page 1 of 1
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Comment: ANOVA like approach of edgeR by Gordon Smyth 52k
To identify common upregulated or downregulated genes, you would need to test for media condition contrasts for each cell type separately, …
Comment: DESeq2 sizefactors counfounded with biological treatment by Anna • 0
Hi James, Apologies (re: posting in the wrong place). Thank you so much for your response, that was exactly the help I needed. Best, A…
Comment: ANOVA like approach of edgeR by Talip ▴ 10
I am comparing the expression patterns of different tissue cell lines (CellType) under five distinct media conditions (Status). Since the c…
Comment: Merge Replicates vs Mixed Model by gabriel.hoffman ▴ 160
It is almost always better to retain the full observed data, if the statistical software is able to model the repeated measures. This is a…
Comment: makeContrastsDream for Interaction by gabriel.hoffman ▴ 160
The simplest way to handle contrasts with an interaction term is to create a new variable. Lets consider a simpler case with variables `Se…
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Answer: Limma- Print-tip loess normalisation-printer layout information does not match M
Answer: Limma- Print-tip loess normalisation-printer layout information does not match M
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
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