Showing : Rsubread • reset
2
votes
4
replies
278
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
updated 2 days ago by ▴ 240 • written 11 days ago by ▴ 60
0
votes
2
replies
157
views
Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
12 weeks ago • updated 11 weeks ago jbono ▴ 10
2
votes
2
replies
174
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3 months ago by ▴ 240 • written 3 months ago by • 0
0
votes
6
replies
259
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
updated 9 weeks ago by ★ 3.3k • written 3 months ago by • 0
0
votes
10
replies
353
views
Rsubread ComplexIndels
complexindelsindels Rsubread
4 months ago • updated 3 months ago Hilary ▴ 20
5
votes
26
replies
2.6k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 6 months ago by ▴ 240 • written 6.3 years ago by 7.6k
0
votes
3
replies
223
views
Rsubread unable to return alignments
Rsubread Alignment
updated 6 months ago by ▴ 240 • written 6 months ago by • 0
5
votes
6
replies
1.5k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 7 months ago by • 0 • written 3.2 years ago by • 0
0
votes
3
replies
933
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 7 months ago by 57k • written 7 months ago by • 0
0
votes
0
replies
105
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
7 months ago martinag.work • 0
5
votes
11
replies
351
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error Rsubread
updated 12 months ago by 43k • written 12 months ago by • 0
2
votes
5
replies
201
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 13 months ago by ★ 3.3k • written 13 months ago by • 0
3
votes
5
replies
238
views
featureCounts chrAliases not working as expected
Rsubread
updated 13 months ago by ▴ 240 • written 14 months ago by • 0
1
vote
2
replies
152
views
Rsubread buildindex error
Rsubread
updated 14 months ago by ★ 3.3k • written 14 months ago by • 0
0
votes
4
replies
268
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 14 months ago by ▴ 240 • written 15 months ago by • 0
0
votes
4
replies
221
views
segfault "memory not mapped" using align from Rsubread
Rsubread align
15 months ago Joseph Fass ▴ 70
4
votes
4
replies
185
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
15 months ago Konstantinos Yeles ▴ 60
0
votes
12
replies
270
views
negative one "-1" values in index files using Rsubread
software error rsubread
updated 15 months ago by ▴ 240 • written 15 months ago by • 0
0
votes
1
reply
159
views
Rsubread: using shared memory for index while aligning with forked processes
rsubread
updated 17 months ago by ★ 3.3k • written 17 months ago by • 0
2
votes
6
replies
371
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 18 months ago by ▴ 240 • written 18 months ago by • 0
5
votes
6
replies
446
views
Rsubread malloc(): memory corruption
Rsubread malloc align
updated 20 months ago by 43k • written 21 months ago by ▴ 60
1
vote
1
reply
242
views
Replicating bowtie2 alignment parameters with Rsubread
Rsubread
updated 20 months ago by ★ 3.3k • written 20 months ago by • 0
2
votes
3
replies
212
views
Rsubread CIGAR output M only?
Rsubread cigar
updated 20 months ago by 43k • written 20 months ago by • 0
2
votes
7
replies
589
views
Rsubread requests longread mode for shotgun RNAseq data
Rsubread counting RNA-seq
updated 2 days ago by ▴ 240 • written 20 months ago by • 0
2
votes
1
reply
343
views
"ERROR: cannot create temp file" when using buildindex from Rsubread
software error Rsubread buildindex
updated 20 months ago by 43k • written 20 months ago by • 0
2
votes
6
replies
1.5k
views
Install Rsubread in win10, failed, how to proceed?
rsubread windows10 rtools
updated 21 months ago by ▴ 240 • written 4.0 years ago by ▴ 200
11
votes
1
reply
359
views
News: Rsubread now available for Windows
rsubread News
22 months ago • updated 21 months ago Gordon Smyth 43k
1
vote
2
replies
847
views
Rsubread package not available?
Rsubread BiocInstaller
updated 21 months ago by 43k • written 9.5 years ago by ▴ 410
4
votes
3
replies
1.1k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 23 months ago by ★ 3.3k • written 23 months ago by ▴ 80
1
vote
3
replies
539
views
Killed 9 on macOS Mojave for Rsubread buildindex
Rsubread buildindex killed 9 Mojave
updated 24 months ago by ★ 3.3k • written 2.0 years ago by • 0
0
votes
1
reply
224
views
Is possible to use NOISeq with counts from RSubread?
noiseq rsubread tophat bowtie bowtie2
2.0 years ago Marcelo Laia ▴ 440
2
votes
3
replies
370
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 2.0 years ago by ★ 3.3k • written 2.0 years ago by ▴ 50
2
votes
1
reply
386
views
Rsubread installation problem
Rsubread BiocParallel
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 10
1
vote
1
reply
222
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 30
3
votes
9
replies
1.1k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 2.1 years ago by ★ 3.3k • written 2.2 years ago by ▴ 100
5
votes
6
replies
456
views
Improving the performance of the align function from Rsubread for old Roche454 reads
align rsubread roche454 rnaseq
updated 2.1 years ago by ★ 3.3k • written 2.2 years ago by ▴ 50
3
votes
7
replies
636
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
4
votes
2
replies
394
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread Rsubread
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 30
7
votes
5
replies
944
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 50
12
votes
7
replies
465
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 2.2 years ago by ▴ 60 • written 2.2 years ago by ▴ 50
2
votes
6
replies
517
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 2.2 years ago by ★ 3.3k • written 2.2 years ago by • 0
1
vote
2
replies
310
views
Problem with importing text file in featureCounts
Rsubread featureCounts
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
3
votes
4
replies
415
views
Featurecount -- normalized Path error
path Rsubread
updated 2.3 years ago by • 0 • written 2.4 years ago by • 0
3
votes
13
replies
919
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
votes
2
replies
692
views
Data import with read.delim
limma rsubread
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
votes
9
replies
754
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
2.5 years ago A ▴ 40
0
votes
9
replies
970
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 2.5 years ago by ★ 3.3k • written 2.5 years ago by ▴ 40
2
votes
1
reply
373
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 2.6 years ago by ★ 3.3k • written 2.6 years ago by ▴ 840
0
votes
16
replies
1.5k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
2.6 years ago writetoroopali • 0
4
votes
7
replies
2.1k
views
convert featureCounts's gene ID to entrez gene id
biomart rsubread gencode
updated 2.7 years ago by 57k • written 2.7 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Research fellow in immunology by Kevin Blighe 3.1k
Hi Alice, could you please modify the question title? - something like '`Help installing flowWorkspace`'
Comment: Research fellow in immunology by ATpoint ▴ 640
Try starting a new R session and then load the package again. If that fails then manually install ellipsis version 0.3.2 or greater. By the…
Answer: Creating the correct model to account for paired-samples (patient-effect) help n by Gordon Smyth 43k
In the limma User's Guide, Section 9.4.1 *Paired Samples* covers paired designs. In the edgeR User's Guide, it is Section 3.4.1.
Comment: How to convert .CEL file to .VCF file? by jesus • 0
Thank you! I'd already seen it, but the problem is that I'm using Windows and I think that code is only for Linux. Thanks anyway!
Comment: DESeq2 codes by Ram ▴ 60
DESeq2 is a piece of software that can be used to find statistically significant differential expression in RNAseq datasets. See: https://b…
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