Showing : featurecounts • reset
7
votes
28
replies
9.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.1 years ago by 53k • written 11.0 years ago by ★ 7.9k
5
votes
10
replies
2.8k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 14 months ago by • 0
6
votes
4
replies
1.8k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 20
3
votes
3
replies
5.3k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
11.1 years ago • updated 11.0 years ago samuel collombet ▴ 140
0
votes
4
replies
5.6k
views
summaries featureCounts output for egeR
featurecounts edger
updated 10.0 years ago by ★ 3.6k • written 10.0 years ago by • 0
3
votes
7
replies
7.4k
views
featureCounts simple (borderline stupid...) question
featurecounts
11.0 years ago Sylvain Foisy ▴ 80
4
votes
3
replies
5.7k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
11.4 years ago gustavoborin01 • 0
4
votes
5
replies
2.3k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts rnaseq subread
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
9
votes
4
replies
3.7k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
11.3 years ago Wei Shi ★ 3.6k
7
votes
4
replies
8.3k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
10.9 years ago beiting ▴ 30
1
vote
4
replies
2.1k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 8.0 years ago by ★ 3.6k • written 8.0 years ago by • 0
0
votes
3
replies
2.5k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
11.1 years ago ccheung • 0
2
votes
14
replies
10k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 3.0 years ago by ▴ 20 • written 8.6 years ago by ▴ 120
2
votes
2
replies
2.6k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 5.0 years ago by ▴ 450 • written 5.0 years ago by • 0
4
votes
3
replies
5.6k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 6.6 years ago by ★ 3.6k • written 6.7 years ago by ▴ 80
4
votes
6
replies
1.8k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
2.1 years ago isaac.vock • 0
3
votes
2
replies
3.9k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 7.6 years ago by 53k • written 7.6 years ago by • 0
1
vote
3
replies
2.5k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
16 months ago yasmin.hilliam ▴ 10
4
votes
7
replies
3.4k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
9.7 years ago myprogramming2016 • 0
4
votes
5
replies
7.3k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 9.8 years ago by ★ 3.6k • written 9.8 years ago by ▴ 180
7
votes
5
replies
5.4k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 60
1
vote
7
replies
7.6k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 9.1 years ago by ★ 3.6k • written 9.1 years ago by ▴ 10
3
votes
7
replies
2.8k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
0
votes
5
replies
2.4k
views
Rsubread, featureCounts misses some exons
annotation featurecounts rsubread
updated 10.5 years ago by 53k • written 10.5 years ago by ▴ 80
3
votes
16
replies
23k
views
featureCounts - paired-end data
featurecounts rsubread
updated 2.7 years ago by • 0 • written 10.8 years ago by ▴ 140
0
votes
2
replies
4.3k
views
lncRNA annotation for featureCouns and STAR
lncRNA featureCounts STAR annotation
updated 7.8 years ago by ★ 3.6k • written 7.8 years ago by ▴ 10
2
votes
4
replies
2.1k
views
featureCounts to RangedSummarizedExperiment
windowcounts featurecounts
updated 9.5 years ago by ★ 29k • written 9.5 years ago by • 0
5
votes
6
replies
7.9k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 4.2 years ago by 53k • written 9.4 years ago by ▴ 20
2
votes
2
replies
3.9k
views
featureCounts Parameters for Exon Junctions
rsubread featureCounts
updated 9.3 years ago by ★ 3.6k • written 9.3 years ago by ★ 1.6k
3
votes
2
replies
3.1k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread featurecounts
updated 8.8 years ago by ★ 3.6k • written 8.8 years ago by ▴ 70
1
vote
2
replies
1.5k
views
DEseq2 analysis for 2 batches of samples that are sequenced separately
deseq2 featurecounts rnaseq
updated 9.6 years ago by 68k • written 9.6 years ago by ▴ 20
3
votes
5
replies
2.3k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts rsubread
9.7 years ago Hadi Gharibi • 0
3
votes
1
reply
3.2k
views
Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 8.3 years ago by ★ 3.6k • written 8.3 years ago by ▴ 20
2
votes
2
replies
2.2k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 23 months ago by • 0 • written 9.7 years ago by ▴ 90
2
votes
1
reply
1.4k
views
Are the endpoints included in intervals for SAF format?
rsubread featurecounts saf
10.8 years ago Ryan C. Thompson ★ 7.9k
2
votes
3
replies
1.9k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 2.9 years ago by 53k • written 7.7 years ago by ▴ 30
1
vote
1
reply
2.6k
views
featureCounts using 3'UTR as genome
featurecounts R
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
0
votes
6
replies
2.7k
views
Rsubread featureCounts with byReadGroup
rsubread featurecounts
updated 8.4 years ago by ▴ 450 • written 8.4 years ago by ▴ 20
0
votes
4
replies
4.6k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
7.9 years ago octopuslegs11 • 0
1
vote
5
replies
4.3k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
3
votes
3
replies
2.5k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 9.8 years ago by ★ 13k • written 9.8 years ago by • 0
0
votes
3
replies
3.6k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread featurecounts exon mRNAseq
updated 8.7 years ago by ★ 3.6k • written 8.7 years ago by ▴ 10
0
votes
2
replies
1.5k
views
negative value for minOverlap parameter
Rsubread minOverlap featureCounts
updated 9.9 years ago by ★ 3.6k • written 9.9 years ago by • 0
7
votes
6
replies
18k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 11.2 years ago by 68k • written 11.2 years ago by ▴ 10
6
votes
6
replies
8.6k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 3.4 years ago by ▴ 200 • written 7.8 years ago by ▴ 10
4
votes
8
replies
2.3k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 8.4 years ago by 53k • written 8.4 years ago by ▴ 20
5
votes
3
replies
7.0k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 8.3 years ago by ★ 3.6k • written 8.3 years ago by ▴ 90
3
votes
1
reply
1.8k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq annotation featurecounts biomart
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 20
4
votes
15
replies
5.7k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 8.2 years ago by 43k • written 8.3 years ago by ▴ 10
0
votes
7
replies
3.1k
views
caught segfault when using featureCounts
rsubread featurecounts
8.2 years ago Ge Tan ▴ 20
137 results • Page 1 of 3
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Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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