Showing : featureCounts • reset
6
votes
26
replies
4.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.8 years ago by ▴ 380 • written 8.5 years ago by 7.8k
6
votes
4
replies
1.1k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 6.7 years ago by 11k • written 6.7 years ago by ▴ 10
3
votes
7
replies
6.0k
views
featureCounts simple (borderline stupid...) question
featurecounts
8.6 years ago Sylvain Foisy ▴ 50
3
votes
3
replies
3.6k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
8.6 years ago samuel collombet ▴ 140
4
votes
3
replies
4.2k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
8.9 years ago gustavoborin01 • 0
0
votes
4
replies
4.9k
views
summaries featureCounts output for egeR
featurecounts edger
updated 7.6 years ago by ★ 3.5k • written 7.6 years ago by • 0
0
votes
3
replies
1.8k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
8.7 years ago ccheung • 0
3
votes
2
replies
2.7k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 5.2 years ago by 48k • written 5.2 years ago by • 0
1
vote
4
replies
1.5k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 5.6 years ago by ★ 3.5k • written 5.6 years ago by • 0
2
votes
14
replies
6.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 7 months ago by • 0 • written 6.1 years ago by ▴ 110
9
votes
4
replies
2.5k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
8.8 years ago Wei Shi ★ 3.5k
4
votes
7
replies
1.8k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
7.3 years ago myprogramming2016 • 0
1
vote
7
replies
4.7k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 6.6 years ago by ★ 3.5k • written 6.6 years ago by ▴ 10
3
votes
7
replies
1.6k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
7
votes
4
replies
6.6k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
8.4 years ago beiting ▴ 30
7
votes
5
replies
3.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 4.5 years ago by 48k • written 4.5 years ago by ▴ 60
4
votes
3
replies
3.8k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.2 years ago by ★ 3.5k • written 4.2 years ago by ▴ 80
2
votes
2
replies
1.4k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 2.6 years ago by ▴ 380 • written 2.6 years ago by • 0
4
votes
5
replies
1.1k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts rnaseq subread
updated 5.1 years ago by 48k • written 5.1 years ago by • 0
4
votes
5
replies
5.5k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 7.3 years ago by ★ 3.5k • written 7.4 years ago by ▴ 180
0
votes
5
replies
1.7k
views
Rsubread, featureCounts misses some exons
annotation featurecounts rsubread
updated 8.0 years ago by 48k • written 8.0 years ago by ▴ 80
2
votes
16
replies
15k
views
featureCounts - paired-end data
featurecounts rsubread
updated 3 months ago by • 0 • written 8.4 years ago by ▴ 140
0
votes
2
replies
2.5k
views
lncRNA annotation for featureCouns and STAR
lncRNA featureCounts STAR annotation
updated 5.3 years ago by ★ 3.5k • written 5.3 years ago by ▴ 10
2
votes
4
replies
1.2k
views
featureCounts to RangedSummarizedExperiment
windowcounts featurecounts
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
1
vote
2
replies
880
views
DEseq2 analysis for 2 batches of samples that are sequenced separately
deseq2 featurecounts rnaseq
updated 7.2 years ago by 63k • written 7.2 years ago by ▴ 20
3
votes
5
replies
1.5k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts rsubread
7.3 years ago Hadi Gharibi • 0
3
votes
1
reply
2.1k
views
Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 5.9 years ago by ★ 3.5k • written 5.9 years ago by • 0
3
votes
6
replies
4.6k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 21 months ago by 48k • written 6.9 years ago by ▴ 20
2
votes
2
replies
2.5k
views
featureCounts Parameters for Exon Junctions
rsubread featureCounts
updated 6.9 years ago by ★ 3.5k • written 6.9 years ago by ★ 1.5k
3
votes
2
replies
2.1k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread featurecounts
updated 6.4 years ago by ★ 3.5k • written 6.4 years ago by ▴ 70
2
votes
2
replies
1.4k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
7.3 years ago • updated 7.2 years ago Jon Manning ▴ 90
2
votes
1
reply
907
views
Are the endpoints included in intervals for SAF format?
rsubread featurecounts saf
8.3 years ago Ryan C. Thompson 7.8k
2
votes
3
replies
1.2k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 6 months ago by 48k • written 5.3 years ago by ▴ 20
1
vote
1
reply
1.7k
views
featureCounts using 3'UTR as genome
featurecounts R
updated 6.1 years ago by 63k • written 6.1 years ago by • 0
0
votes
6
replies
1.6k
views
Rsubread featureCounts with byReadGroup
rsubread featurecounts
updated 6.0 years ago by ▴ 380 • written 6.0 years ago by ▴ 20
0
votes
4
replies
2.9k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
5.4 years ago octopuslegs11 • 0
3
votes
3
replies
1.8k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 7.4 years ago by 13k • written 7.4 years ago by • 0
0
votes
3
replies
2.6k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread featurecounts exon mRNAseq
updated 6.3 years ago by ★ 3.5k • written 6.3 years ago by ▴ 10
0
votes
2
replies
897
views
negative value for minOverlap parameter
Rsubread minOverlap featureCounts
updated 7.5 years ago by ★ 3.5k • written 7.5 years ago by • 0
7
votes
6
replies
15k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 8.8 years ago by 63k • written 8.8 years ago by ▴ 10
1
vote
5
replies
2.6k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 6.1 years ago by 63k • written 6.1 years ago by • 0
4
votes
6
replies
5.1k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 11 months ago by ▴ 20 • written 5.4 years ago by ▴ 10
4
votes
3
replies
4.8k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 5.9 years ago by ★ 3.5k • written 5.9 years ago by ▴ 80
0
votes
7
replies
2.1k
views
caught segfault when using featureCounts
rsubread featurecounts
5.8 years ago Ge Tan ▴ 20
0
votes
3
replies
1.1k
views
FeatureCounts --read2pos option
featurecounts
updated 6.5 years ago by ★ 3.5k • written 6.5 years ago by • 0
4
votes
8
replies
1.1k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 5.9 years ago by 48k • written 5.9 years ago by • 0
2
votes
4
replies
4.7k
views
featureCounts (sourceforge) not returning any counts in count table, even though summary indicates reads were assigned?
featurecounts software error
7.6 years ago Darya Vanichkina ▴ 120
3
votes
1
reply
1.0k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq annotation featurecounts biomart
updated 5.9 years ago by 63k • written 5.9 years ago by • 0
4
votes
15
replies
3.7k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 5.8 years ago by 40k • written 5.9 years ago by ▴ 10
0
votes
1
reply
1.4k
views
dataset TxDb.Mmusculus.UCSC.mm9.knownGene shows other gene_id then genome browser
rsubread featurecounts
updated 8.0 years ago by 63k • written 8.0 years ago by ▴ 80
50 results • Page 1 of 1
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Answer: DelayedArray::read_sparse_block by Hervé Pagès 16k
Hi Koki, Sorry again for the slow response. `read_sparse_block()` has been around for years. It's a generic function defined in the *…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Votes
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
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