Showing : htseqtools • reset
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Which library now contains the ssdCoverage command that used to be found in the htseqtools package for R version 4.0.1 ?
Deprecation chipseq htseqtools Bioconductor
updated 4.9 years ago by ▴ 780 • written 4.9 years ago by • 0
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HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools deseq2 counts cuffdiff
9.9 years ago Jon Bråte ▴ 270
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4
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htSeqTools errors
Coverage htSeqTools Coverage htSeqTools
updated 13.9 years ago by ★ 6.8k • written 13.9 years ago by ▴ 80
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GenomicRanges requires a IRanges version not available in the repository
GenomicRanges htSeqTools GenomicRanges htSeqTools
updated 13.9 years ago by 6.7k • written 13.9 years ago by ▴ 80
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htSeqTools - filtered reads > BED?
IRanges htSeqTools IRanges htSeqTools
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ▴ 70
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htSeqTools: using GRanges and GRangesList
convert htSeqTools convert htSeqTools
14.0 years ago Oscar Reina ▴ 20
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htSeqTools - naming RangedData objects?
htSeqTools ASSIGN htSeqTools ASSIGN
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ▴ 70
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
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It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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I updated the above answer today.
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I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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