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rsubread
•
reset
1
vote
21
replies
3.4k
views
Rsubread stopping half-way through align
rsubread
7.8 years ago • updated 7.7 years ago
Campbell.1933
• 0
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 11 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
10
replies
2.5k
views
Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
Rsubread
updated 7.7 years ago by
Wei Shi
★ 3.6k • written 7.9 years ago by
MWSchmid
• 0
0
votes
11
replies
2.1k
views
Rsubread/Rsamtools mappings outside of chromosome ranges
PROcess
Rsamtools
Rsubread
TCC
PROcess
Rsamtools
Rsubread
TCC
12.2 years ago
Thomas Girke
★ 1.7k
0
votes
5
replies
1.7k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis
Annotation
GO
BSgenome
cdf
BSgenome
Rsubread
Annotation
GO
BSgenome
cdf
BSgenome
10.7 years ago
Alan Smith
▴ 150
2
votes
6
replies
2.5k
views
Install Rsubread in win10, failed, how to proceed?
rsubread
windows10
rtools
updated 4.6 years ago by
Yang Liao
▴ 380 • written 6.8 years ago by
Yisong Zhen
▴ 200
3
votes
8
replies
7.1k
views
Reads in Unassigned_NoFeatures category produced by featureCounts
rsubread
updated 8.1 years ago by
Wei Shi
★ 3.6k • written 8.1 years ago by
Likai Mao
▴ 40
4
votes
3
replies
4.6k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq
rsubread
featurecounts
r
9.5 years ago
gustavoborin01
• 0
2
votes
4
replies
1.5k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Christopher
• 0
0
votes
5
replies
1.6k
views
Rsubread crash on Mac during alignment
software error
rsubread
7.2 years ago • updated 6.9 years ago
raf4
▴ 20
3
votes
3
replies
4.1k
views
Rsubreads - featureCount - gtf - error
rsubread
featurecounts
9.2 years ago
samuel collombet
▴ 140
1
vote
11
replies
2.5k
views
rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
rsubread
BWA
NGS
updated 7.6 years ago by
Wei Shi
★ 3.6k • written 7.7 years ago by
tarek.mohamed
▴ 10
1
vote
3
replies
2.0k
views
Error using RSubread to buildIndex with large Fasta
rsubread
updated 9.1 years ago by
Wei Shi
★ 3.6k • written 9.1 years ago by
beiting
▴ 30
6
votes
3
replies
2.1k
views
Possible bug in Rsubread Phred-Score read
rsubread
bug
alignment
updated 9.5 years ago by
Wei Shi
★ 3.6k • written 9.5 years ago by
caufeminecraft
▴ 20
0
votes
15
replies
2.9k
views
Rsubread crashes in 32bit linux
Yeast
Rsubread
Yeast
Rsubread
updated 11.9 years ago by
Wei Shi
★ 3.6k • written 11.9 years ago by
Robert Castelo
★ 3.3k
0
votes
5
replies
1.8k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
BiocViews
VariantAnnotation
Annotation
biocViews
Rsubread
VariantAnnotation
gmapR
BiocViews
10.4 years ago
Thomas Girke
★ 1.7k
12
votes
7
replies
1.9k
views
No method for coercing this S4 class to a vector, as trying to import my own data rather than using SRA in the workflow RnaSeqGeneEdgeRQL
rnaseqgeneedgerql
shortread
Rsubread
updated 5.1 years ago by
Aspie96
▴ 60 • written 5.1 years ago by
Raito92
▴ 60
9
votes
16
replies
2.8k
views
Rsubread install fails, "unable to load shared object Rsubread.so"
rsubread
5.9 years ago
jet456
▴ 10
2
votes
3
replies
672
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago
Gerhard Thallinger
▴ 180
1
vote
5
replies
1.3k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by
Gordon Smyth
50k • written 24 months ago by
J-E
• 0
2
votes
2
replies
1.8k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.1 years ago by
Yang Liao
▴ 380 • written 3.1 years ago by
Jason
• 0
1
vote
2
replies
255
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
2
votes
3
replies
903
views
Rsubread CIGAR output M only?
Rsubread
cigar
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
lauren.fitch
• 0
1
vote
3
replies
1.4k
views
Killed 9 on macOS Mojave for Rsubread buildindex
Rsubread
buildindex
killed 9
Mojave
updated 4.8 years ago by
Wei Shi
★ 3.6k • written 4.9 years ago by
raabec
• 0
7
votes
5
replies
3.8k
views
featureCounts returning a matrix of counts full of 0...
featureCounts
rnaseq
Rsubread
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Raito92
▴ 60
4
votes
10
replies
5.2k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm
gene length
count matrix
edgeR
rsubread
8.5 years ago
AB
▴ 110
2
votes
8
replies
2.8k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 2.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
am39
• 0
5
votes
11
replies
1.6k
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error
Rsubread
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
barrel0luck
• 0
4
votes
3
replies
4.3k
views
Rsubread, Error in featureCounts paired end
Rsubread
paired end
featureCounts
updated 4.8 years ago by
Wei Shi
★ 3.6k • written 4.8 years ago by
hauken_heyken
▴ 80
0
votes
2
replies
1.7k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 2.5 years ago by
Yang Liao
▴ 380 • written 2.5 years ago by
mruffalo
• 0
2
votes
6
replies
2.5k
views
featureCount error - cannot identify gene_id
dexseq
rsubread
featureCount
software error
updated 4.4 years ago by
Yang Liao
▴ 380 • written 4.4 years ago by
seung.ho.steven.choi
• 0
13
votes
20
replies
3.5k
views
cellCounts() function floating point error
Rsubread
24 months ago • updated 21 months ago
J-E
• 0
7
votes
4
replies
6.9k
views
Low percentage of assigned fragments with FeatureCounts
rsubread
featurecounts
rnaseq
9.0 years ago
beiting
▴ 30
1
vote
4
replies
1.7k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq
rsubread
featurecounts
updated 6.2 years ago by
Wei Shi
★ 3.6k • written 6.2 years ago by
mmurshed
• 0
0
votes
4
replies
1.1k
views
Is circular RNA read out as linear fragments during Rsubread-DESeq2
deseq2
circrna
rsubread
updated 5.9 years ago by
Wei Shi
★ 3.6k • written 5.9 years ago by
csijst
• 0
0
votes
2
replies
2.5k
views
counting RNA-seq reads in R/BioC
GO
Infrastructure
Rsubread
easyRNASeq
GO
Infrastructure
Rsubread
easyRNASeq
updated 11.6 years ago by
Valerie Obenchain
★ 6.8k • written 11.6 years ago by
Mark Robinson
▴ 880
9
votes
4
replies
2.8k
views
News:
Experimental data package 'seqc'
seqc
rsubread
featurecounts
subjunc
ercc
News
9.4 years ago
Wei Shi
★ 3.6k
1
vote
2
replies
1.7k
views
Rsubread package not available?
Rsubread
BiocInstaller
updated 4.7 years ago by
Gordon Smyth
50k • written 12.4 years ago by
Noah Dowell
▴ 410
6
votes
5
replies
2.4k
views
reads alignment statistics
rsubread
bioconductor
updated 6.6 years ago by
Hervé Pagès
16k • written 6.6 years ago by
C T
▴ 140
4
votes
7
replies
5.9k
views
convert featureCounts's gene ID to entrez gene id
biomart
rsubread
gencode
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
YinCY
▴ 20
0
votes
4
replies
2.2k
views
Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
rsubread
ncbi
GRCh38
hg38
updated 7.5 years ago by
Wei Shi
★ 3.6k • written 7.5 years ago by
jan.soderman
• 0
1
vote
3
replies
3.5k
views
rsubread featurecounts returns 0% successfully assigned reads
rsubread
updated 8.7 years ago by
amoltej
▴ 10 • written 9.2 years ago by
ross.chapman
▴ 10
1
vote
10
replies
5.0k
views
Rsubread package not available? Warning resolved
affxparser
Rsubread
BiocInstaller
affxparser
Rsubread
BiocInstaller
updated 12.4 years ago by
Wei Shi
★ 3.6k • written 12.4 years ago by
NDowell
▴ 20
0
votes
8
replies
2.0k
views
Rsubread alingner
Alignment
Yeast
Rsubread
Alignment
Yeast
Rsubread
13.0 years ago
Wei Shi
★ 3.6k
3
votes
4
replies
1.5k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread
rnaseq
alignment
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
thomas.dobrenel
• 0
3
votes
3
replies
5.2k
views
Run featureCounts in isoform/transcript level in Rsubread
rsubread
updated 8.2 years ago by
Wei Shi
★ 3.6k • written 8.2 years ago by
Likai Mao
▴ 40
3
votes
5
replies
5.6k
views
Problem while installing Rsubread
installation
rsubread
updated 8.2 years ago by
James W. MacDonald
65k • written 8.2 years ago by
jackeikee
• 0
2
votes
9
replies
1.7k
views
countPrimaryAlignmentsOnly=TRUE produced more counts
rsubread
updated 8.2 years ago by
Wei Shi
★ 3.6k • written 8.2 years ago by
Likai Mao
▴ 40
3
votes
7
replies
1.9k
views
Rsubread inbuilt annotation
rsubread
featureCounts
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
diego.carvalhoalvarez
• 0
3
votes
4
replies
964
views
Featurecount -- normalized Path error
path
Rsubread
updated 5.2 years ago by
cellfixnowusa
• 0 • written 5.3 years ago by
memoly101
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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