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
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 4 weeks ago by • 0 • written 7.9 years ago by ▴ 90
2
votes
3
replies
253
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 5 weeks ago by ★ 3.6k • written 5 weeks ago by • 0
0
votes
1
reply
183
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 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 ★ 3.6k • written 12 weeks ago by • 0
1
vote
1
reply
391
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 8 weeks ago by ▴ 380 • written 3 months ago by ▴ 10
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 50k • written 9.2 years ago by ★ 7.9k
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
0
votes
4
replies
440
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 3 months ago by 50k • written 3 months ago by • 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 50k • written 5 months ago by • 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 8 months ago by 50k • written 8 months ago by • 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 ★ 3.6k • written 8 months ago by • 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 65k • written 9 months ago by • 0
0
votes
1
reply
487
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 9 months ago by 65k • written 9 months ago by • 0
1
vote
6
replies
1.8k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 9 months ago by ▴ 380 • written 4.1 years ago by • 0
1
vote
1
reply
662
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
0
votes
2
replies
583
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts rsubread
updated 10 months ago by • 0 • written 9.0 years ago by ▴ 140
0
votes
1
reply
865
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 12 months ago by ★ 3.6k • written 12 months ago by • 0
1
vote
5
replies
1.4k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by 50k • written 2.0 years ago by • 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 ★ 3.6k • written 17 months ago by • 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 50k • written 14 months ago by • 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 50k • written 15 months ago by • 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 50k • written 11.9 years ago by ★ 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 50k • written 18 months ago by • 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
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 23 months ago by 50k • written 23 months ago by • 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 ★ 4.1k • written 23 months ago by ▴ 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
1.4k
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
2
votes
8
replies
2.9k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 2.0 years ago by ★ 3.3k • written 4.0 years ago by • 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 ▴ 10 • written 5.0 years ago by ▴ 120
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 50k • written 2.1 years ago by • 0
2
votes
1
reply
1.0k
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 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 ▴ 380 • written 2.2 years ago by • 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
France, 12 minutes ago
WEHI, Melbourne, Australia, 15 minutes ago
Sweden, 32 minutes ago
Japan, 51 minutes ago
EMBL Heidelberg, 1 hour ago
Traffic: 427 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