Showing : featureCounts • reset
3
votes
16
replies
20k
views
featureCounts - paired-end data
featurecounts rsubread
updated 20 months ago by • 0 • written 9.8 years ago by ▴ 140
7
votes
6
replies
17k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 10.1 years ago by 68k • written 10.1 years ago by ▴ 10
2
votes
14
replies
8.8k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 24 months ago by ▴ 20 • written 7.5 years ago by ▴ 120
2
votes
2
replies
7.7k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.1 years ago Chise ▴ 10
7
votes
4
replies
7.5k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
9.8 years ago beiting ▴ 30
7
votes
28
replies
7.3k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 12 months ago by 52k • written 9.9 years ago by ★ 7.9k
6
votes
6
replies
7.1k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 2.3 years ago by ▴ 200 • written 6.8 years ago by ▴ 10
3
votes
7
replies
6.7k
views
featureCounts simple (borderline stupid...) question
featurecounts
10.0 years ago Sylvain Foisy ▴ 80
4
votes
5
replies
6.6k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 8.7 years ago by ★ 3.6k • written 8.8 years ago by ▴ 180
5
votes
6
replies
6.6k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 3.1 years ago by 52k • written 8.3 years ago by ▴ 20
5
votes
3
replies
6.4k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 7.2 years ago by ★ 3.6k • written 7.2 years ago by ▴ 90
1
vote
5
replies
6.3k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 18 months ago by ▴ 450 • written 3.6 years ago by ▴ 10
1
vote
7
replies
6.3k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 8.0 years ago by ★ 3.6k • written 8.0 years ago by ▴ 10
4
votes
4
replies
6.0k
views
FeatureCounts
counts subread RNASeq featurecounts
3.3 years ago k___ ▴ 30
3
votes
5
replies
5.6k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 10.0 years ago by ▴ 450 • written 10.0 years ago by ▴ 20
2
votes
4
replies
5.5k
views
featureCounts (sourceforge) not returning any counts in count table, even though summary indicates reads were assigned?
featurecounts software error
9.0 years ago Darya Vanichkina ▴ 130
4
votes
2
replies
5.5k
views
featureCounts for multiple features
featurecounts
updated 2.3 years ago by ▴ 20 • written 6.6 years ago by ▴ 10
0
votes
4
replies
5.4k
views
summaries featureCounts output for egeR
featurecounts edger
updated 9.0 years ago by ★ 3.6k • written 9.0 years ago by • 0
4
votes
3
replies
5.2k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
10.3 years ago gustavoborin01 • 0
3
votes
3
replies
5.1k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
4
votes
3
replies
5.0k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 5.6 years ago by ★ 3.6k • written 5.6 years ago by ▴ 80
4
votes
15
replies
4.9k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 7.2 years ago by 43k • written 7.3 years ago by ▴ 10
3
votes
3
replies
4.8k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
10.0 years ago samuel collombet ▴ 140
3
votes
11
replies
4.7k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.8 years ago Sarah_piggy ▴ 10
5
votes
11
replies
4.6k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 2.8 years ago by ▴ 10 • written 5.8 years ago by ▴ 120
7
votes
5
replies
4.6k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 60
0
votes
1
reply
4.5k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
1
vote
2
replies
4.3k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.9 years ago chatterjee.arumoy ▴ 10
0
votes
2
replies
4.3k
views
Problem running featurecounts in Rsubread on GFF file
rsubread featurecounts gff Grch38.p7 vs hg38
7.7 years ago raf4 ▴ 30
0
votes
2
replies
4.3k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.6 years ago by ▴ 80
0
votes
8
replies
4.1k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread featurecounts
6.7 years ago connor.geraghty • 0
0
votes
4
replies
3.9k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
6.8 years ago octopuslegs11 • 0
0
votes
2
replies
3.8k
views
DEXSeq on FeatureCounts output
dexseq featurecounts
9.4 years ago Vivek.b ▴ 100
0
votes
6
replies
3.7k
views
Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
deseq2 featurecounts error message
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
5
replies
3.7k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
1
vote
1
reply
3.6k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 5.8 years ago by ★ 3.6k • written 5.8 years ago by ▴ 10
0
votes
2
replies
3.6k
views
lncRNA annotation for featureCouns and STAR
lncRNA featureCounts STAR annotation
updated 6.7 years ago by ★ 3.6k • written 6.7 years ago by ▴ 10
0
votes
9
replies
3.5k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 6.2 years ago by ★ 3.6k • written 6.2 years ago by ▴ 40
3
votes
13
replies
3.5k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 6.1 years ago by 52k • written 6.1 years ago by • 0
3
votes
2
replies
3.4k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
1
vote
2
replies
3.4k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 5.6 years ago by 52k • written 5.6 years ago by • 0
2
votes
2
replies
3.3k
views
featureCounts Parameters for Exon Junctions
rsubread featureCounts
updated 8.3 years ago by ★ 3.6k • written 8.3 years ago by ★ 1.6k
0
votes
1
reply
3.2k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
9
votes
4
replies
3.2k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
10.2 years ago Wei Shi ★ 3.6k
0
votes
3
replies
3.2k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread featurecounts exon mRNAseq
updated 7.7 years ago by ★ 3.6k • written 7.7 years ago by ▴ 10
4
votes
7
replies
3.1k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 20
1
vote
1
reply
3.0k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
0
votes
3
replies
2.9k
views
featureCount and bam
featurecounts
7.6 years ago Morris ▴ 10
1
vote
1
reply
2.8k
views
Warning using feuture count related to GTF file
featurecounts
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
3
votes
1
reply
2.8k
views
Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 7.3 years ago by ★ 3.6k • written 7.3 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: GSVA on RNAseq data by Robert Castelo ★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell by James W. MacDonald 68k
Put it in a list and put the list in a column.
Comment: For some reason I can't update BiocManager to 3.20 by James W. MacDonald 68k
Please post output from starting R and then running `sessionInfo()` (as requested by the web form you use to post questions). I get ``` > …
Comment: p-value the same for different contrasts DESeq2 by caroline.zanchi • 0
It would be great if it were possible to do something similar using GlmGamPoi !
Comment: Web accessibility of Bioconductor.org by Sean Davis 21k
Added issue to website github repo: https://github.com/Bioconductor/bioconductor.org/issues/304
Votes
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
A: Rtracklayer fails to export TxDb as GFF3 without CDS
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