Showing : featureCounts • reset
9
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4
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2.5k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
8.8 years ago Wei Shi ★ 3.5k
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
6
replies
15k
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featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 8.8 years ago by 63k • written 8.8 years ago by ▴ 10
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
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
5
votes
11
replies
3.2k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 17 months ago by ▴ 10 • written 4.4 years ago by ▴ 120
4
votes
2
replies
3.9k
views
featureCounts for multiple features
featurecounts
updated 10 months ago by ▴ 20 • written 5.2 years ago by ▴ 10
4
votes
2
replies
924
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.0 years ago by ★ 1.3k • written 4.0 years ago by • 0
4
votes
4
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3.6k
views
FeatureCounts
counts subread RNASeq featurecounts
22 months ago k___ ▴ 20
4
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5
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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
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
4
votes
7
replies
1.8k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
7.3 years ago myprogramming2016 • 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
4
votes
8
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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
4
votes
5
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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
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
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
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
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
4
votes
7
replies
2.3k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 5.3 years ago by 40k • written 5.3 years ago by ▴ 20
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
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
3
votes
3
replies
3.6k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
8.6 years ago samuel collombet ▴ 140
3
votes
3
replies
1.2k
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
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
7
replies
1.6k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
3
votes
13
replies
2.4k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 4.7 years ago by 48k • written 4.7 years ago by • 0
3
votes
2
replies
1.8k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq featureCounts STAR minMQS mapping quality score
updated 4.6 years ago by 48k • written 4.6 years ago by ▴ 20
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
3
votes
5
replies
4.4k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 8.6 years ago by ▴ 380 • written 8.6 years ago by ▴ 20
3
votes
7
replies
6.0k
views
featureCounts simple (borderline stupid...) question
featurecounts
8.6 years ago Sylvain Foisy ▴ 50
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
3
votes
11
replies
2.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
17 months ago • updated 16 months ago Sarah_piggy ▴ 10
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
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
2
votes
2
replies
444
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
11 months ago dario.beraldi • 0
2
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4
replies
1.2k
views
featureCounts to RangedSummarizedExperiment
windowcounts featurecounts
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
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
16
replies
15k
views
featureCounts - paired-end data
featurecounts rsubread
updated 3 months ago by • 0 • written 8.4 years ago by ▴ 140
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
3
replies
651
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
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
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
2
votes
2
replies
4.2k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
21 months ago Chise ▴ 10
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
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
2
votes
6
replies
1.5k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 4.5 years ago by ★ 3.5k • written 4.5 years ago by • 0
2
votes
3
replies
1.6k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 3.8 years ago by 63k • written 3.8 years ago by • 0
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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