Showing : featureCounts • reset
7
votes
28
replies
7.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 15 months ago by 52k • written 10.2 years ago by ★ 7.9k
5
votes
10
replies
2.1k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 5 months ago by • 0
6
votes
4
replies
1.6k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 20
3
votes
3
replies
4.9k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
10.3 years ago • updated 10.2 years ago samuel collombet ▴ 140
0
votes
4
replies
5.5k
views
summaries featureCounts output for egeR
featurecounts edger
updated 9.2 years ago by ★ 3.6k • written 9.3 years ago by • 0
3
votes
7
replies
7.0k
views
featureCounts simple (borderline stupid...) question
featurecounts
10.3 years ago Sylvain Foisy ▴ 80
4
votes
3
replies
5.4k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
10.6 years ago gustavoborin01 • 0
4
votes
5
replies
1.8k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts rnaseq subread
updated 6.7 years ago by 52k • written 6.7 years ago by • 0
9
votes
4
replies
3.3k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
10.5 years ago Wei Shi ★ 3.6k
7
votes
4
replies
7.7k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
10.1 years ago beiting ▴ 30
1
vote
4
replies
1.9k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 7.2 years ago by ★ 3.6k • written 7.2 years ago by • 0
0
votes
3
replies
2.3k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
10.4 years ago ccheung • 0
2
votes
14
replies
9.3k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 2.2 years ago by ▴ 20 • written 7.8 years ago by ▴ 120
2
votes
2
replies
2.4k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 4.2 years ago by ▴ 450 • written 4.2 years ago by • 0
4
votes
3
replies
5.3k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 5.8 years ago by ★ 3.6k • written 5.9 years ago by ▴ 80
4
votes
6
replies
1.3k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
16 months ago • updated 15 months ago isaac.vock • 0
3
votes
2
replies
3.6k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 6.9 years ago by 52k • written 6.9 years ago by • 0
1
vote
3
replies
1.4k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
7 months ago yasmin.hilliam ▴ 10
4
votes
7
replies
2.9k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
9.0 years ago myprogramming2016 • 0
4
votes
5
replies
6.8k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 9.0 years ago by ★ 3.6k • written 9.1 years ago by ▴ 180
7
votes
5
replies
5.0k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 6.1 years ago by 52k • written 6.1 years ago by ▴ 60
1
vote
7
replies
6.7k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 8.3 years ago by ★ 3.6k • written 8.3 years ago by ▴ 10
3
votes
7
replies
2.5k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 6.1 years ago by 52k • written 6.1 years ago by • 0
0
votes
5
replies
2.2k
views
Rsubread, featureCounts misses some exons
annotation featurecounts rsubread
updated 9.7 years ago by 52k • written 9.7 years ago by ▴ 80
3
votes
16
replies
21k
views
featureCounts - paired-end data
featurecounts rsubread
updated 23 months ago by • 0 • written 10.0 years ago by ▴ 140
0
votes
2
replies
3.9k
views
lncRNA annotation for featureCouns and STAR
lncRNA featureCounts STAR annotation
updated 7.0 years ago by ★ 3.6k • written 7.0 years ago by ▴ 10
2
votes
4
replies
1.9k
views
featureCounts to RangedSummarizedExperiment
windowcounts featurecounts
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
5
votes
6
replies
7.1k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 3.4 years ago by 52k • written 8.6 years ago by ▴ 20
2
votes
2
replies
3.5k
views
featureCounts Parameters for Exon Junctions
rsubread featureCounts
updated 8.6 years ago by ★ 3.6k • written 8.6 years ago by ★ 1.6k
3
votes
2
replies
2.8k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread featurecounts
updated 8.1 years ago by ★ 3.6k • written 8.1 years ago by ▴ 70
1
vote
2
replies
1.3k
views
DEseq2 analysis for 2 batches of samples that are sequenced separately
deseq2 featurecounts rnaseq
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 20
3
votes
5
replies
2.0k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts rsubread
8.9 years ago Hadi Gharibi • 0
3
votes
1
reply
2.9k
views
Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 7.6 years ago by ★ 3.6k • written 7.6 years ago by ▴ 20
2
votes
2
replies
2.0k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 13 months ago by • 0 • written 8.9 years ago by ▴ 90
2
votes
1
reply
1.2k
views
Are the endpoints included in intervals for SAF format?
rsubread featurecounts saf
10.0 years ago Ryan C. Thompson ★ 7.9k
2
votes
3
replies
1.7k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 2.2 years ago by 52k • written 6.9 years ago by ▴ 20
1
vote
1
reply
2.4k
views
featureCounts using 3'UTR as genome
featurecounts R
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
votes
6
replies
2.4k
views
Rsubread featureCounts with byReadGroup
rsubread featurecounts
updated 7.6 years ago by ▴ 450 • written 7.6 years ago by ▴ 20
0
votes
4
replies
4.2k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
7.1 years ago octopuslegs11 • 0
1
vote
5
replies
3.9k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
3
votes
3
replies
2.3k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 9.1 years ago by ★ 13k • written 9.1 years ago by • 0
0
votes
3
replies
3.3k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread featurecounts exon mRNAseq
updated 8.0 years ago by ★ 3.6k • written 8.0 years ago by ▴ 10
0
votes
2
replies
1.3k
views
negative value for minOverlap parameter
Rsubread minOverlap featureCounts
updated 9.1 years ago by ★ 3.6k • written 9.1 years ago by • 0
7
votes
6
replies
18k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 10.4 years ago by 68k • written 10.4 years ago by ▴ 10
6
votes
6
replies
7.7k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 2.6 years ago by ▴ 200 • written 7.0 years ago by ▴ 10
4
votes
8
replies
2.0k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 7.6 years ago by 52k • written 7.6 years ago by ▴ 20
5
votes
3
replies
6.6k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 7.5 years ago by ★ 3.6k • written 7.5 years ago by ▴ 90
3
votes
1
reply
1.6k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq annotation featurecounts biomart
updated 7.6 years ago by 68k • written 7.6 years ago by ▴ 20
4
votes
15
replies
5.1k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 7.5 years ago by 43k • written 7.6 years ago by ▴ 10
0
votes
7
replies
2.9k
views
caught segfault when using featureCounts
rsubread featurecounts
7.4 years ago Ge Tan ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
Without including the row names for the heatmap, it's impossible to know if the directionality is switched or not. Do note that the orderin…
Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0
![Figure1][1]![Figure2][2] [1]: /media/images/d62918c5-2886-44ae-930d-91d292c3 [2]: /media/images/421df232-8a9c-4016-bc4a-431ca57a
Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
Ah yes sorry :) But then I still do not understand why is it that on the plot I attached, the gene definitely has non-0 counts in less than…
Answer: Typo in the help of lmFit() by Gordon Smyth 52k
Thanks for the heads-up. > The _Details_ in the documentation of lmFit() still says that the default correlation is 0.75 Yes, you're righ…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by caroline.zanchi ▴ 10
Thank you ! ![enter image description here][1] In the end I did ```r rn2 <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "GENENAME"…
Votes
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
Awards • All
Scholar to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to AMgroup • 0
Popular Question to favorov • 0
Popular Question to bhanu.chandra1 • 0
Locations • All
United States, 13 minutes ago
United Kingdom, 15 minutes ago
United Kingdom, 19 minutes ago
United States, 23 minutes ago
United States, 40 minutes ago
Traffic: 3286 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6