Showing : rsubread • reset
0
votes
0
replies
33
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
3 days ago kthapa • 0
0
votes
2
replies
151
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
17 days ago Gerhard Thallinger ▴ 180
0
votes
0
replies
72
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 21 days ago by 48k • written 23 days ago by • 0
2
votes
3
replies
361
views
Rsubread: subjunc() loads index repeatedly
Rsubread
10 weeks ago • updated 6 weeks ago Gerhard Thallinger ▴ 180
0
votes
2
replies
205
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 7 weeks ago by ★ 3.5k • written 7 weeks ago by • 0
0
votes
2
replies
226
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 7 weeks ago by 63k • written 7 weeks ago by • 0
0
votes
1
reply
168
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 8 weeks ago by 63k • written 8 weeks ago by • 0
1
vote
1
reply
272
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 weeks ago by ▴ 380 • written 9 weeks ago by • 0
0
votes
2
replies
250
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 3 months ago by ★ 3.4k • written 3 months ago by • 0
0
votes
1
reply
346
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 4 months ago by ★ 3.5k • written 5 months ago by • 0
0
votes
0
replies
209
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
5 months ago barrypraveen • 0
1
vote
3
replies
376
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
6 months ago rmoorehe • 0
2
votes
9
replies
872
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
6 months ago Hilary ▴ 30
0
votes
2
replies
504
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 6 months ago by ★ 3.5k • written 10 months ago by • 0
2
votes
4
replies
771
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 7 months ago by 48k • written 7 months ago by • 0
0
votes
0
replies
212
views
Rsubread align every slow in mac but faster in windows
Rsubread
8 months ago Wei • 0
3
votes
3
replies
1.3k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 8 months ago by 48k • written 8 months ago by • 0
2
votes
3
replies
667
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 10 months ago by 48k • written 10 months ago by • 0
0
votes
2
replies
585
views
Rsubread align --R session aborts
RNA Alignment Rsubread
14 months ago • updated 13 months ago sreekalasn • 0
13
votes
20
replies
2.8k
views
cellCounts() function floating point error
Rsubread
16 months ago • updated 14 months ago J-E • 0
0
votes
1
reply
653
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 16 months ago by ★ 3.4k • written 16 months ago by ▴ 10
1
vote
1
reply
1.0k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 16 months ago by 48k • written 16 months ago by • 0
1
vote
5
replies
987
views
Case Studies Data Missing in Rsubread
Rsubread
updated 5 months ago by 48k • written 17 months ago by • 0
1
vote
4
replies
958
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
17 months ago Chise ▴ 10
1
vote
2
replies
689
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
17 months ago Chise ▴ 10
3
votes
11
replies
2.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
17 months ago Sarah_piggy ▴ 10
0
votes
1
reply
574
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 17 months ago by 48k • written 17 months ago by • 0
2
votes
1
reply
746
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 18 months ago by 48k • written 18 months ago by ▴ 20
0
votes
1
reply
604
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 19 months ago by ▴ 380 • written 19 months ago by • 0
1
vote
5
replies
1.4k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
19 months ago Lucy ▴ 60
5
votes
6
replies
2.3k
views
Error in Rsubread featureCounts
Rsubread
19 months ago Zhaoxu • 0
2
votes
2
replies
4.3k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
21 months ago Chise ▴ 10
0
votes
2
replies
1.3k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 23 months ago by ▴ 380 • written 23 months ago by • 0
1
vote
8
replies
2.5k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
23 months ago • updated 22 months ago v.merino.nicolas ▴ 10
0
votes
1
reply
631
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 23 months ago by ★ 3.5k • written 23 months ago by • 0
2
votes
2
replies
1.0k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 2.2 years ago by 48k • written 2.3 years ago by • 0
4
votes
5
replies
1.6k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.3 years ago • updated 2.2 years ago Konstantinos Yeles ▴ 80
0
votes
2
replies
917
views
Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
2.5 years ago jbono ▴ 10
2
votes
2
replies
1.5k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 2.6 years ago by ▴ 380 • written 2.6 years ago by • 0
0
votes
6
replies
1.4k
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
updated 2.5 years ago by ★ 3.5k • written 2.6 years ago by • 0
0
votes
10
replies
1.2k
views
Rsubread ComplexIndels
complexindelsindels Rsubread
2.6 years ago Hilary ▴ 30
6
votes
26
replies
4.9k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.8 years ago by ▴ 380 • written 8.6 years ago by 7.8k
0
votes
3
replies
1.3k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 2.8 years ago by ▴ 380 • written 2.8 years ago by • 0
5
votes
6
replies
3.6k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 2.9 years ago by • 0 • written 5.5 years ago by • 0
0
votes
3
replies
6.3k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 2.9 years ago by 63k • written 2.9 years ago by • 0
0
votes
0
replies
551
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
2.9 years ago martinag.work • 0
5
votes
11
replies
1.2k
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error Rsubread
updated 3.3 years ago by 48k • written 3.3 years ago by • 0
2
votes
8
replies
2.1k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 17 months ago by ★ 3.0k • written 3.4 years ago by • 0
3
votes
5
replies
1.2k
views
featureCounts chrAliases not working as expected
Rsubread
updated 3.4 years ago by ▴ 380 • written 3.4 years ago by • 0
1
vote
2
replies
1.5k
views
Rsubread buildindex error
Rsubread
updated 3.5 years ago by ★ 3.5k • written 3.5 years ago by • 0
50 results • Page 1 of 1
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Comment: ComBat_seq function in sva package does not return a matrix by Federico ▴ 10
Thanks for your help, problem solved :)
Answer: ComBat_seq function in sva package does not return a matrix by ATpoint ★ 3.4k
That happens if your `x` is a data.frame rather than a matrix. It is listed under the Q&A section in https://github.com/zhangyuqing/ComBat-…
Answer: error running exp2grn by Fabricio Almeida-Silva ▴ 40
Hi, Adriana. It seems like the gene IDs you specified in `Host13tfs$Protein.ID` do not match any gene IDs in the row names of your expr…
Comment: Singlecell protein surface (ADT) pseudotime techniques by EspressoKris ▴ 10
I was thinking that they may not perform as well due to the low number of features and derived PCs. But I haven't tried them yet so I am un…
Comment: Singlecell protein surface (ADT) pseudotime techniques by ATpoint ★ 3.4k
How is this different from a "normal" pseudotime tracking other that in your case you give the ADT count matrix rather than the RNA matrix …
Votes
ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
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