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Showing :
rsubread
•
reset
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
25 days ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
285
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
7 weeks ago • updated 4 weeks ago
isaac.vock
• 0
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
271
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 7 weeks ago by
Wei Shi
★ 3.6k • written 7 weeks ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
199
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
0
replies
158
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
10 weeks ago
chris2.a.white
• 0
1
vote
1
reply
293
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 10 weeks ago by
Wei Shi
★ 3.6k • written 3 months ago by
Alex
• 0
1
vote
1
reply
413
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 10 weeks ago by
Yang Liao
▴ 380 • written 3 months ago by
Joe Marturano
▴ 10
0
votes
0
replies
173
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
11 weeks ago
thomas.heigl.ibk
• 0
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
4
votes
6
replies
782
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago
isaac.vock
• 0
0
votes
4
replies
474
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
tjgray4
• 0
1
vote
2
replies
289
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
0
votes
1
reply
347
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
glopez
• 0
2
votes
2
replies
625
views
Long-read mode in featureCounts
Rsubread
LongRead
7 months ago
mmisak
• 0
0
votes
2
replies
1.3k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
7 months ago
Gregory
• 0
0
votes
0
replies
304
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
7 months ago
kthapa
• 0
0
votes
2
replies
537
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
8 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
334
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Cosmin Saveanu
• 0
2
votes
3
replies
713
views
Rsubread: subjunc() loads index repeatedly
Rsubread
10 months ago • updated 9 months ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
634
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 9 months ago by
Wei Shi
★ 3.6k • written 9 months ago by
amanda.gutierrez
• 0
0
votes
2
replies
1.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
vitoriastavis
• 0
0
votes
1
reply
505
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread
ensembldb
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
Ya
• 0
1
vote
6
replies
1.9k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 9 months ago by
Yang Liao
▴ 380 • written 4.2 years ago by
bryan.penning
• 0
1
vote
1
reply
684
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 10 months ago by
Yang Liao
▴ 380 • written 10 months ago by
StevenE.Strong
• 0
0
votes
2
replies
612
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 11 months ago by
ATpoint
★ 4.1k • written 11 months ago by
Sukeerthi
• 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
0
votes
1
reply
884
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 12 months ago by
Wei Shi
★ 3.6k • written 12 months ago by
Carlos
• 0
1
vote
5
replies
1.4k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 13 months ago by
Gordon Smyth
50k • written 2.0 years ago by
J-E
• 0
0
votes
0
replies
432
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
13 months ago
barrypraveen
• 0
1
vote
3
replies
822
views
Correct script for featurecounts in Rsubread
Rsubread
Rsu
14 months ago
rmoorehe
• 0
2
votes
9
replies
1.7k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0
featureCounts
T2T
Rsubread
14 months ago
Hilary
▴ 30
0
votes
2
replies
879
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread
featureCounts
updated 14 months ago by
Wei Shi
★ 3.6k • written 17 months ago by
Konstantin
• 0
2
votes
4
replies
1.6k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Christopher
• 0
0
votes
0
replies
417
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 months ago
Wei
• 0
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
0
votes
1
reply
2.8k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 16 months ago by
Gordon Smyth
50k • written 12.0 years ago by
Kasper Daniel Hansen
★ 6.5k
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
0
votes
2
replies
847
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
21 months ago
sreekalasn
• 0
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
2.0 years ago • updated 22 months ago
J-E
• 0
1
vote
1
reply
1.5k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 24 months ago by
Gordon Smyth
50k • written 2.0 years ago by
margo
• 0
0
votes
1
reply
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 2.0 years ago by
ATpoint
★ 4.1k • written 2.0 years ago by
johnmcma
▴ 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
1
vote
4
replies
1.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
2.1 years ago
Chise
▴ 10
1
vote
2
replies
995
views
Aliases of drosophila gene names
Drosophila
Rsubread
dm6
2.1 years ago
Chise
▴ 10
2
votes
8
replies
2.9k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
am39
• 0
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
0
votes
1
reply
830
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
efernandez
• 0
2
votes
1
reply
1.0k
views
Can Rsubread output use Ensembl gene IDs
Ensembl
Rsubread
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
agustin.gonvi
▴ 20
0
votes
1
reply
849
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread
Alignment
updated 2.2 years ago by
Yang Liao
▴ 380 • written 2.2 years ago by
amytam2014
• 0
50 results • Page
1 of 1
Recent ...
Replies
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…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
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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