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Rsubread
•
reset
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
24 months ago • updated 21 months ago
J-E
• 0
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
11
votes
1
reply
1.1k
views
News:
Rsubread now available for Windows
rsubread
News
4.7 years ago
Gordon Smyth
50k
9
votes
16
replies
2.8k
views
Rsubread install fails, "unable to load shared object Rsubread.so"
rsubread
5.9 years ago
jet456
▴ 10
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
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
28
replies
6.1k
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
4
replies
6.9k
views
Low percentage of assigned fragments with FeatureCounts
rsubread
featurecounts
rnaseq
9.1 years ago
beiting
▴ 30
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
6
votes
5
replies
2.4k
views
reads alignment statistics
rsubread
bioconductor
updated 6.6 years ago by
Hervé Pagès
16k • written 6.7 years ago by
C T
▴ 140
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
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
5
votes
6
replies
4.3k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 3.5 years ago by
bjwiley23
• 0 • written 6.1 years ago by
juls
• 0
5
votes
11
replies
3.9k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread
featureCounts
updated 2.0 years ago by
Sarah_piggy
▴ 10 • written 5.0 years ago by
k.vitting.seerup
▴ 120
5
votes
6
replies
1.6k
views
Rsubread malloc(): memory corruption
Rsubread
malloc
align
updated 4.5 years ago by
Gordon Smyth
50k • written 4.7 years ago by
Konstantinos Yeles
▴ 80
5
votes
6
replies
1.4k
views
Improving the performance of the align function from Rsubread for old Roche454 reads
align
rsubread
roche454
rnaseq
updated 5.0 years ago by
Wei Shi
★ 3.6k • written 5.0 years ago by
Raito92
▴ 60
5
votes
6
replies
3.2k
views
Error in Rsubread featureCounts
Rsubread
2.2 years ago
Zhaoxu
• 0
5
votes
1
reply
3.3k
views
Tutorial:
Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread
rsubread
ensembldb
Tutorial
8.1 years ago
phil.chapman
▴ 150
4
votes
3
replies
5.5k
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
▴ 80
4
votes
6
replies
749
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
1
reply
4.6k
views
Rsubread featureCounts with strand information
Rsubread
bam
rnaseq
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
rubi
▴ 110
4
votes
5
replies
2.1k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread
featurecounts
coercion
2.9 years ago • updated 2.8 years ago
Konstantinos Yeles
▴ 80
4
votes
4
replies
1.6k
views
Issues loading a BAM file resulted from featurecounts
featurecount
rsubread
GenomicAlignments
4.1 years ago
Konstantinos Yeles
▴ 80
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
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
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
4
votes
10
replies
5.3k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm
gene length
count matrix
edgeR
rsubread
8.6 years ago • updated 8.5 years ago
AB
▴ 110
4
votes
2
replies
1.2k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Jonathan Griffiths
▴ 90
3
votes
4
replies
2.6k
views
nthreads option does NOT work in rsubread featureCounts
rsubread
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
shao
▴ 100
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
6
replies
5.4k
views
How featureCounts define the gene length
featurecounts
rnaseq
rsubread
updated 2.3 years ago by
Gordon Smyth
50k • written 7.6 years ago by
Yiwei Niu
▴ 20
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
16
replies
18k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 10 months ago by
Robert
• 0 • written 9.0 years ago by
samuel collombet
▴ 140
3
votes
5
replies
1.5k
views
featureCounts chrAliases not working as expected
Rsubread
updated 4.0 years ago by
Yang Liao
▴ 380 • written 4.0 years ago by
kathleen.e.grogan
• 0
3
votes
5
replies
4.9k
views
Error with featureCounts
featurecounts
rnaseq
rsubread
updated 9.2 years ago by
Yang Liao
▴ 380 • written 9.2 years ago by
syrttgump
▴ 20
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
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
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
3
replies
2.7k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Sara
• 0
3
votes
5
replies
5.7k
views
Problem while installing Rsubread
installation
rsubread
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
jackeikee
• 0
3
votes
1
reply
1.5k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error
rsubread
alignment
updated 8.4 years ago by
Wei Shi
★ 3.6k • written 8.4 years ago by
Thomas Carroll
▴ 420
3
votes
4
replies
1.4k
views
File not found error when using dupRadar::analyzeDuprates
dupradar
rsubread
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
b.nota
▴ 360
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
1
reply
1.5k
views
Use BAM file created from subjunc function (Rsubread package) for feature counts?
rsubread
subjunc
updated 8.7 years ago by
Wei Shi
★ 3.6k • written 8.7 years ago by
Stephen Piccolo
▴ 590
3
votes
4
replies
968
views
Featurecount -- normalized Path error
path
Rsubread
updated 5.2 years ago by
cellfixnowusa
• 0 • written 5.3 years ago by
memoly101
• 0
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 8.2 years ago by
Likai Mao
▴ 40
3
votes
8
replies
4.3k
views
Fraction arguments for multi mapping reads in featureCounts in Rsubread
rsubread
8.4 years ago
tg369
▴ 10
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
1
reply
1.9k
views
Rsubread installation problem
Rsubread
BiocParallel
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
agustin.gonvi
▴ 20
2
votes
3
replies
1.4k
views
Boxplot function not showing all reads length on x-axis
boxplot
reads
fastq
sequencing
rsubread
updated 4.9 years ago by
Wei Shi
★ 3.6k • written 4.9 years ago by
Raito92
▴ 60
50 results • Page
1 of 1
Recent ...
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Answer: Once again a "Model matrix not full rank"
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swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
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50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
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50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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Comment: CombineArrays for EPIC and EPIC V2
by
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• 0
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