Showing : featureCounts • reset
0
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problem running featurecounts using hg38 in-built annotation
featurecounts hg38
8.4 years ago raf4 ▴ 30
0
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2
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4.6k
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Problem running featurecounts in Rsubread on GFF file
rsubread featurecounts gff Grch38.p7 vs hg38
8.4 years ago raf4 ▴ 30
0
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5
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2.9k
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FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 2.3 years ago by ▴ 450 • written 8.4 years ago by • 0
3
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2
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3.0k
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Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread featurecounts
updated 8.5 years ago by ★ 3.6k • written 8.5 years ago by ▴ 70
0
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3
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1.9k
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FeatureCounts --read2pos option
featurecounts
updated 8.6 years ago by ★ 3.6k • written 8.6 years ago by • 0
0
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1
reply
1.5k
views
% of assigned reads using Rsubread featureCounts useMetaFeatures
featurecounts rsubread
8.6 years ago IV ▴ 30
0
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1
reply
1.8k
views
IRanges object from count matrix
genomicranges iranges featurecounts counts rnaseq
updated 8.7 years ago by 16k • written 8.7 years ago by ★ 1.5k
1
vote
7
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7.0k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 8.7 years ago by ★ 3.6k • written 8.7 years ago by ▴ 10
6
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4
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1.7k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 20
2
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2
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3.6k
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featureCounts Parameters for Exon Junctions
rsubread featureCounts
updated 9.0 years ago by ★ 3.6k • written 9.0 years ago by ★ 1.6k
5
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6
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7.4k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 3.8 years ago by 53k • written 9.0 years ago by ▴ 20
0
votes
1
reply
1.7k
views
FeatureCounts Assertion `l_name < 100' failed.
featurecounts rnaseq
9.1 years ago shg018 • 0
2
votes
4
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2.0k
views
featureCounts to RangedSummarizedExperiment
windowcounts featurecounts
updated 9.2 years ago by ★ 29k • written 9.2 years ago by • 0
1
vote
2
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1.4k
views
DEseq2 analysis for 2 batches of samples that are sequenced separately
deseq2 featurecounts rnaseq
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 20
2
votes
2
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2.1k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 19 months ago by • 0 • written 9.4 years ago by ▴ 90
3
votes
5
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2.2k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts rsubread
9.4 years ago • updated 9.3 years ago Hadi Gharibi • 0
4
votes
7
replies
3.1k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
9.4 years ago myprogramming2016 • 0
4
votes
5
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6.9k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 9.4 years ago by ★ 3.6k • written 9.5 years ago by ▴ 180
3
votes
3
replies
2.4k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 9.5 years ago by ★ 13k • written 9.5 years ago by • 0
0
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2
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1.4k
views
negative value for minOverlap parameter
Rsubread minOverlap featureCounts
updated 9.6 years ago by ★ 3.6k • written 9.6 years ago by • 0
0
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4
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5.6k
views
summaries featureCounts output for egeR
featurecounts edger
updated 9.7 years ago by ★ 3.6k • written 9.7 years ago by • 0
2
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4
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5.8k
views
featureCounts (sourceforge) not returning any counts in count table, even though summary indicates reads were assigned?
featurecounts software error
9.7 years ago Darya Vanichkina ▴ 130
0
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1
reply
2.0k
views
RSubread 0% mapping
rsubread mapping featurecounts align
9.9 years ago Jo ▴ 30
0
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5
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2.3k
views
Rsubread, featureCounts misses some exons
annotation featurecounts rsubread
updated 10.1 years ago by 53k • written 10.1 years ago by ▴ 80
0
votes
1
reply
1.8k
views
dataset TxDb.Mmusculus.UCSC.mm9.knownGene shows other gene_id then genome browser
rsubread featurecounts
updated 10.1 years ago by 68k • written 10.1 years ago by ▴ 80
0
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2
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4.1k
views
DEXSeq on FeatureCounts output
dexseq featurecounts
10.1 years ago Vivek.b ▴ 100
2
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1
reply
1.3k
views
Are the endpoints included in intervals for SAF format?
rsubread featurecounts saf
10.4 years ago Ryan C. Thompson ★ 7.9k
3
votes
16
replies
22k
views
featureCounts - paired-end data
featurecounts rsubread
updated 2.4 years ago by • 0 • written 10.5 years ago by ▴ 140
7
votes
4
replies
7.9k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
10.5 years ago beiting ▴ 30
3
votes
3
replies
5.1k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
10.7 years ago samuel collombet ▴ 140
3
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7
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7.2k
views
featureCounts simple (borderline stupid...) question
featurecounts
10.7 years ago Sylvain Foisy ▴ 80
3
votes
5
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6.0k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 10.7 years ago by ▴ 450 • written 10.7 years ago by ▴ 20
0
votes
3
replies
2.4k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
10.8 years ago ccheung • 0
7
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6
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18k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 10.8 years ago by 68k • written 10.8 years ago by ▴ 10
9
votes
4
replies
3.4k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
10.9 years ago Wei Shi ★ 3.6k
4
votes
3
replies
5.5k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
11.0 years ago gustavoborin01 • 0
136 results • Page 3 of 3
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
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Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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