Showing : Rsubread • reset
0
votes
5
replies
178
views
cellCounts() function floating point error
Rsubread
updated 1 day ago by ★ 3.3k • written 10 days ago by • 0
0
votes
5
replies
207
views
Case Studies Data Missing in Rsubread
Rsubread
14 days ago • updated 10 days ago J-E • 0
1
vote
4
replies
157
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
18 days ago • updated 15 days ago Chise ▴ 10
1
vote
2
replies
132
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
16 days ago • updated 15 days ago Chise ▴ 10
3
votes
11
replies
355
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
4 weeks ago • updated 15 days ago Sarah_piggy ▴ 10
0
votes
1
reply
142
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 5 weeks ago by 45k • written 5 weeks ago by • 0
2
votes
1
reply
123
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 7 weeks ago by 45k • written 7 weeks ago by ▴ 10
0
votes
1
reply
150
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 10 weeks ago by ▴ 340 • written 10 weeks ago by • 0
1
vote
5
replies
357
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3 months ago Lucy ▴ 50
5
votes
6
replies
355
views
Error in Rsubread featureCounts
Rsubread
3 months ago Zhaoxu • 0
2
votes
2
replies
724
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
4 months ago Chise ▴ 10
0
votes
2
replies
290
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 6 months ago by ▴ 340 • written 6 months ago by • 0
1
vote
8
replies
797
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
6 months ago v.merino.nicolas ▴ 10
0
votes
1
reply
217
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 6 months ago by ★ 3.3k • written 6 months ago by • 0
2
votes
2
replies
374
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 10 months ago by 45k • written 10 months ago by • 0
4
votes
5
replies
658
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
11 months ago • updated 10 months ago Konstantinos Yeles ▴ 70
0
votes
2
replies
397
views
Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
13 months ago jbono ▴ 10
2
votes
2
replies
631
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 14 months ago by ▴ 340 • written 14 months ago by • 0
0
votes
6
replies
644
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
updated 13 months ago by ★ 3.3k • written 14 months ago by • 0
0
votes
10
replies
661
views
Rsubread ComplexIndels
complexindelsindels Rsubread
15 months ago • updated 14 months ago Hilary ▴ 20
6
votes
26
replies
3.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 17 months ago by ▴ 340 • written 7.2 years ago by 7.8k
0
votes
3
replies
582
views
Rsubread unable to return alignments
Rsubread Alignment
updated 17 months ago by ▴ 340 • written 17 months ago by • 0
5
votes
6
replies
2.2k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 18 months ago by • 0 • written 4.1 years ago by • 0
0
votes
3
replies
3.2k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 18 months ago by 59k • written 18 months ago by • 0
0
votes
0
replies
272
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
18 months ago martinag.work • 0
5
votes
11
replies
616
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error Rsubread
updated 23 months ago by 45k • written 23 months ago by • 0
2
votes
8
replies
654
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 21 days ago by ★ 2.8k • written 2.0 years ago by • 0
3
votes
5
replies
650
views
featureCounts chrAliases not working as expected
Rsubread
updated 2.0 years ago by ▴ 340 • written 2.1 years ago by • 0
1
vote
2
replies
707
views
Rsubread buildindex error
Rsubread
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by • 0
0
votes
4
replies
588
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 2.1 years ago by ▴ 340 • written 2.2 years ago by • 0
0
votes
4
replies
449
views
segfault "memory not mapped" using align from Rsubread
Rsubread align
2.1 years ago Joseph Fass ▴ 70
4
votes
4
replies
388
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
2.2 years ago Konstantinos Yeles ▴ 70
0
votes
12
replies
535
views
negative one "-1" values in index files using Rsubread
software error rsubread
updated 2.2 years ago by ▴ 340 • written 2.2 years ago by • 0
0
votes
1
reply
278
views
Rsubread: using shared memory for index while aligning with forked processes
rsubread
updated 2.4 years ago by ★ 3.3k • written 2.4 years ago by • 0
2
votes
6
replies
957
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 2.4 years ago by ▴ 340 • written 2.5 years ago by • 0
5
votes
6
replies
784
views
Rsubread malloc(): memory corruption
Rsubread malloc align
updated 2.6 years ago by 45k • written 2.7 years ago by ▴ 70
1
vote
1
reply
435
views
Replicating bowtie2 alignment parameters with Rsubread
Rsubread
updated 2.6 years ago by ★ 3.3k • written 2.6 years ago by • 0
2
votes
3
replies
379
views
Rsubread CIGAR output M only?
Rsubread cigar
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
2
votes
7
replies
1.1k
views
Rsubread requests longread mode for shotgun RNAseq data
Rsubread counting RNA-seq
updated 11 months ago by ▴ 340 • written 2.6 years ago by • 0
2
votes
5
replies
993
views
"ERROR: cannot create temp file" when using buildindex from Rsubread
software error Rsubread buildindex
updated 8 months ago by ▴ 340 • written 2.6 years ago by • 0
2
votes
6
replies
1.8k
views
Install Rsubread in win10, failed, how to proceed?
rsubread windows10 rtools
updated 2.7 years ago by ▴ 340 • written 4.9 years ago by ▴ 200
11
votes
1
reply
563
views
News: Rsubread now available for Windows
rsubread News
2.7 years ago Gordon Smyth 45k
1
vote
2
replies
1.0k
views
Rsubread package not available?
Rsubread BiocInstaller
updated 2.7 years ago by 45k • written 10.5 years ago by ▴ 410
4
votes
3
replies
2.3k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 2.8 years ago by ★ 3.3k • written 2.9 years ago by ▴ 80
1
vote
3
replies
800
views
Killed 9 on macOS Mojave for Rsubread buildindex
Rsubread buildindex killed 9 Mojave
updated 2.9 years ago by ★ 3.3k • written 2.9 years ago by • 0
0
votes
1
reply
360
views
Is possible to use NOISeq with counts from RSubread?
noiseq rsubread tophat bowtie bowtie2
2.9 years ago Marcelo Laia ▴ 450
2
votes
3
replies
667
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 2.9 years ago by ★ 3.3k • written 3.0 years ago by ▴ 60
2
votes
1
reply
798
views
Rsubread installation problem
Rsubread BiocParallel
updated 3.0 years ago by 45k • written 3.0 years ago by ▴ 10
1
vote
1
reply
363
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 3.0 years ago by 45k • written 3.0 years ago by ▴ 30
5
votes
11
replies
1.8k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 4 weeks ago by ▴ 10 • written 3.1 years ago by ▴ 100
50 results • Page 1 of 1
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Replies
Comment: Variance explained (coefficient of determination) in edgeR by Gordon Smyth 45k
No, you have it wrong way around. If you want deviance explained by x1, then you need ``` R2_x1 <- ( deviance without x1 in model - devia…
Comment: Variance explained (coefficient of determination) in edgeR by Gemma • 0
Many thanks for your answer. To clarify the last point, `R2_nox1` is the proportion of the deviance explained when considering `design.no…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by Rory Stark ★ 4.4k
The latest version, `DiffBind_3.6.1`, contains fixes for these issues. You will get these fixes if you upgrade to `R_4.2.0` and `Bioconduct…
Comment: Variance explained (coefficient of determination) in edgeR by Gordon Smyth 45k
The R2 values look completely normal. The median R2 is 10%, which seems somewhat low rather than high. With so many genes, you will natural…
Comment: Variance explained (coefficient of determination) in edgeR by Gemma • 0
Many thanks, that seems to work! However, the estimates tend to be surprisingly high, for many genes R2 being close to 1 (quartiles being…
Votes
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
Answer: Use MulticoreParam under BatchtoolsParam
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
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