Showing : featureCounts • reset
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
23 days ago • updated 20 days ago Gordon Smyth 48k
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2
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207
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 6 weeks ago by 63k • written 6 weeks ago by • 0
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1
reply
262
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featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 weeks ago by ▴ 380 • written 9 weeks ago by • 0
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1
reply
332
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Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 4 months ago by ★ 3.5k • written 4 months ago by • 0
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202
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
5 months ago barrypraveen • 0
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9
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833
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featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
6 months ago Hilary ▴ 30
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2
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492
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 6 months ago by ★ 3.5k • written 9 months ago by • 0
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253
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Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
7 months ago yao hua • 0
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1
reply
402
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Subread installation on Linux ARM64
subread featureCounts
updated 7 months ago by ▴ 380 • written 7 months ago by • 0
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277
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DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2 featurecounts
updated 7 months ago by ★ 1.3k • written 7 months ago by • 0
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1.3k
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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
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1
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993
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 9 months ago by ★ 1.3k • written 9 months ago by • 0
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1
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1.0k
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Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 10 months ago by 48k • written 10 months ago by • 0
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300
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Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 10 months ago by ★ 3.4k • written 10 months ago by • 0
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3
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651
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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
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2
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444
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featureCounts: No effect of setting -d and -D?
subread featureCounts
11 months ago dario.beraldi • 0
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302
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
11 months ago rridley3 • 0
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2
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1.1k
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featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 11 months ago by • 0 • written 2.1 years ago by • 0
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5
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3.5k
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featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 8 weeks ago by ▴ 380 • written 2.2 years ago by ▴ 10
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2
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3.9k
views
featureCounts for multiple features
featurecounts
updated 10 months ago by ▴ 20 • written 5.2 years ago by ▴ 10
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3
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1.2k
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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
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6
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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
2
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14
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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
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5
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1.9k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 10 weeks ago by ▴ 380 • written 6.4 years ago by • 0
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
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Comment: List of Deprecated Packages for Bioc3.18 by Hervé Pagès 16k
Also the source package is not available [in BioC 3.17](https://bioconductor.org/packages/3.17/CancerInSilico) which means that the package…
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.
Votes
Comment: List of Deprecated Packages for Bioc3.18
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
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