Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Rsubread
•
reset
0
votes
0
replies
78
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
9 days ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
254
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 14 days ago
isaac.vock
• 0
2
votes
3
replies
253
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 5 weeks ago by
Wei Shi
★ 3.6k • written 5 weeks ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
183
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
0
replies
143
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
8 weeks ago
chris2.a.white
• 0
1
vote
1
reply
264
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 8 weeks ago by
Wei Shi
★ 3.6k • written 12 weeks ago by
Alex
• 0
0
votes
0
replies
159
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
9 weeks ago
thomas.heigl.ibk
• 0
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
1
vote
1
reply
391
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 8 weeks ago by
Yang Liao
▴ 380 • written 3 months ago by
Joe Marturano
▴ 10
0
votes
4
replies
440
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
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
1
vote
2
replies
267
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
0
votes
1
reply
323
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
glopez
• 0
2
votes
2
replies
588
views
Long-read mode in featureCounts
Rsubread
LongRead
6 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
292
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
7 months ago
kthapa
• 0
0
votes
2
replies
516
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
320
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 7 months ago by
Gordon Smyth
50k • written 8 months ago by
Cosmin Saveanu
• 0
2
votes
3
replies
684
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
601
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 8 months ago by
Wei Shi
★ 3.6k • written 8 months ago by
amanda.gutierrez
• 0
0
votes
2
replies
1.0k
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
487
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
1
reply
662
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 9 months ago by
StevenE.Strong
• 0
0
votes
2
replies
583
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
Sukeerthi
• 0
0
votes
1
reply
865
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
0
votes
0
replies
422
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
12 months ago
barrypraveen
• 0
1
vote
3
replies
790
views
Correct script for featurecounts in Rsubread
Rsubread
Rsu
13 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
857
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 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Christopher
• 0
0
votes
0
replies
407
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 months ago
Wei
• 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
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
836
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
21 months ago • updated 20 months ago
sreekalasn
• 0
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
24 months ago • updated 21 months ago
J-E
• 0
0
votes
1
reply
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 23 months ago by
ATpoint
★ 4.1k • written 23 months ago by
johnmcma
▴ 10
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
margo
• 0
1
vote
5
replies
1.4k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by
Gordon Smyth
50k • written 2.0 years ago by
J-E
• 0
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
2.0 years ago
Chise
▴ 10
1
vote
2
replies
985
views
Aliases of drosophila gene names
Drosophila
Rsubread
dm6
2.0 years ago
Chise
▴ 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
0
votes
1
reply
816
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
836
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
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.2 years ago
Lucy
▴ 60
5
votes
6
replies
3.2k
views
Error in Rsubread featureCounts
Rsubread
2.2 years ago
Zhaoxu
• 0
2
votes
2
replies
5.9k
views
"Paired-end reads were detected in single-end read library"
featureCounts
Rsubread
2.4 years ago
Chise
▴ 10
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
1
vote
8
replies
3.2k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
2.5 years ago
v.merino.nicolas
▴ 10
0
votes
1
reply
855
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 2.5 years ago by
Wei Shi
★ 3.6k • written 2.5 years ago by
sha-ked
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
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
Gordon Smyth
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
by
Gordon Smyth
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?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
• 0
Popular Question
to
Theo
▴ 10
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Locations
• All
EMBL Heidelberg,
9 minutes ago
France,
12 minutes ago
The city by the bay,
36 minutes ago
WEHI, Melbourne, Australia,
47 minutes ago
Iran,
1 hour ago
Traffic: 523 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