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Showing :
featureCounts
•
reset
9
votes
4
replies
2.8k
views
News:
Experimental data package 'seqc'
seqc
rsubread
featurecounts
subjunc
ercc
News
9.5 years ago
Wei Shi
★ 3.6k
7
votes
28
replies
6.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 3 months ago by
Gordon Smyth
50k • written 9.2 years ago by
Ryan C. Thompson
★ 7.9k
7
votes
5
replies
3.8k
views
featureCounts returning a matrix of counts full of 0...
featureCounts
rnaseq
Rsubread
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
Raito92
▴ 60
7
votes
6
replies
16k
views
featureCount - very less Successfully assigned reads
featurecounts
rsubread
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
amoltej
▴ 10
7
votes
4
replies
7.0k
views
Low percentage of assigned fragments with FeatureCounts
rsubread
featurecounts
rnaseq
9.1 years ago
beiting
▴ 30
6
votes
4
replies
1.3k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges
genomicranges
featurecounts
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
s1437643
▴ 20
5
votes
11
replies
3.9k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread
featureCounts
updated 2.1 years ago by
Sarah_piggy
▴ 10 • written 5.1 years ago by
k.vitting.seerup
▴ 120
5
votes
3
replies
5.6k
views
Rsubread counting peaks ATACseq
Rsubread
atac-seq
narrowpeaks
featurecounts
updated 6.5 years ago by
Wei Shi
★ 3.6k • written 6.5 years ago by
j.bergenstrahle
▴ 90
4
votes
5
replies
1.4k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
rogangrant
• 0
4
votes
7
replies
2.2k
views
RNAseq reads mapped to the gene
star
featurecounts
edgeR
RNAseq
8.0 years ago
myprogramming2016
• 0
4
votes
15
replies
4.2k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2
rnaseq
featurecounts
DESeqDataSetFromMatrix
updated 6.5 years ago by
Michael Love
42k • written 6.6 years ago by
bioinf
▴ 10
4
votes
7
replies
2.6k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq
deseq2
featurecounts
differential binding analysis
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
hkarakurt
▴ 20
4
votes
3
replies
4.7k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq
rsubread
featurecounts
r
9.6 years ago
gustavoborin01
• 0
4
votes
2
replies
4.6k
views
featureCounts for multiple features
featurecounts
updated 18 months ago by
hermidalc
▴ 20 • written 5.9 years ago by
hwu12
▴ 10
4
votes
5
replies
6.1k
views
Hisat2 vs featureCounts summary statistics
featurecounts
hisat2
rna-seq
mapping
updated 8.0 years ago by
Wei Shi
★ 3.6k • written 8.0 years ago by
Koen Van den Berge
▴ 180
4
votes
3
replies
4.4k
views
Rsubread, Error in featureCounts paired end
Rsubread
paired end
featureCounts
updated 4.8 years ago by
Wei Shi
★ 3.6k • written 4.9 years ago by
hauken_heyken
▴ 80
4
votes
6
replies
783
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago
isaac.vock
• 0
4
votes
5
replies
2.2k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread
featurecounts
coercion
3.0 years ago • updated 2.8 years ago
Konstantinos Yeles
▴ 80
4
votes
2
replies
1.2k
views
bwa mem to feature Counts
bwa mem
featureCounts
updated 4.6 years ago by
swbarnes2
★ 1.4k • written 4.6 years ago by
ajajoo
• 0
4
votes
6
replies
6.1k
views
strange results with featureCounts
RNA-seq
featureCounts
total RNA
updated 19 months ago by
snijesh
▴ 20 • written 6.0 years ago by
inah
▴ 10
4
votes
8
replies
1.5k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq
featurecounts
edger
deseq2
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
Jack
• 0
4
votes
4
replies
5.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
3
votes
2
replies
2.4k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 7.1 years ago by
Wei Shi
★ 3.6k • written 7.1 years ago by
jma1991
▴ 70
3
votes
6
replies
5.4k
views
How featureCounts define the gene length
featurecounts
rnaseq
rsubread
updated 2.4 years ago by
Gordon Smyth
50k • written 7.6 years ago by
Yiwei Niu
▴ 20
3
votes
3
replies
4.1k
views
Rsubreads - featureCount - gtf - error
rsubread
featurecounts
9.3 years ago • updated 9.2 years ago
samuel collombet
▴ 140
3
votes
3
replies
2.8k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Sara
• 0
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 11 months ago by
Robert
• 0 • written 9.0 years ago by
samuel collombet
▴ 140
3
votes
5
replies
1.7k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts
rsubread
7.9 years ago
Hadi Gharibi
• 0
3
votes
1
reply
2.5k
views
Explainnation of featureCounts in-built annotation?
rnaseq
annotation
featurecounts
updated 6.6 years ago by
Wei Shi
★ 3.6k • written 6.6 years ago by
Jack
• 0
3
votes
7
replies
1.9k
views
Rsubread inbuilt annotation
rsubread
featureCounts
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
diego.carvalhoalvarez
• 0
3
votes
13
replies
3.0k
views
Rsubread- feature counts
annotation
Rsubread
featureCounts
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
memoly101
• 0
3
votes
2
replies
2.1k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq
featureCounts
STAR
minMQS
mapping quality score
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
Gary
▴ 20
3
votes
1
reply
1.3k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq
annotation
featurecounts
biomart
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
Jack
• 0
3
votes
3
replies
1.9k
views
read counts of paired end reads for DESeq2 analysis
deseq
featurecounts
paired
updated 8.1 years ago by
Steve Lianoglou
★ 13k • written 8.1 years ago by
tszn1984
• 0
3
votes
5
replies
4.9k
views
Error with featureCounts
featurecounts
rnaseq
rsubread
updated 9.3 years ago by
Yang Liao
▴ 380 • written 9.3 years ago by
syrttgump
▴ 20
3
votes
7
replies
6.3k
views
featureCounts simple (borderline stupid...) question
featurecounts
9.3 years ago
Sylvain Foisy
▴ 80
3
votes
2
replies
3.1k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 5.8 years ago by
Gordon Smyth
50k • written 5.9 years ago by
jennyl.smith12
• 0
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.1 years ago • updated 2.0 years ago
Sarah_piggy
▴ 10
2
votes
2
replies
2.8k
views
featureCounts Parameters for Exon Junctions
rsubread
featureCounts
updated 7.5 years ago by
Wei Shi
★ 3.6k • written 7.6 years ago by
Dario Strbenac
★ 1.5k
2
votes
2
replies
787
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
19 months ago
dario.beraldi
• 0
2
votes
4
replies
1.5k
views
featureCounts to RangedSummarizedExperiment
windowcounts
featurecounts
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
karl.nordstrom
• 0
2
votes
1
reply
1.0k
views
Are the endpoints included in intervals for SAF format?
rsubread
featurecounts
saf
9.0 years ago
Ryan C. Thompson
★ 7.9k
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 7 weeks ago by
isaac.vock
• 0 • written 7.9 years ago by
Jon Manning
▴ 90
2
votes
3
replies
1.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 18 months ago by
Gordon Smyth
50k • written 18 months ago by
Jon
• 0
2
votes
14
replies
7.6k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 15 months ago by
Chris
▴ 10 • written 6.8 years ago by
Biologist
▴ 110
2
votes
2
replies
1.9k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.2 years ago by
Yang Liao
▴ 380 • written 3.2 years ago by
Jason
• 0
2
votes
2
replies
6.0k
views
"Paired-end reads were detected in single-end read library"
featureCounts
Rsubread
2.4 years ago
Chise
▴ 10
2
votes
3
replies
1.4k
views
How edgeR reads an R List object produced by featureCounts
edger
featurecounts
updated 14 months ago by
Gordon Smyth
50k • written 5.9 years ago by
Gary
▴ 20
2
votes
4
replies
5.1k
views
featureCounts (sourceforge) not returning any counts in count table, even though summary indicates reads were assigned?
featurecounts
software error
8.3 years ago
Darya Vanichkina
▴ 120
2
votes
6
replies
1.9k
views
featurecounts Rsubread ERROR on exon_id
R
error
software error
Rsubread
featurecounts
updated 5.1 years ago by
Wei Shi
★ 3.6k • written 5.1 years ago by
edejong
• 0
50 results • Page
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
jane
• 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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