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Rsubread Read Bam and filter reads by TAG field
Rsubread featurecounts featurerequest
8.0 years ago alessandro.pastore ▴ 20
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Tab on Main menu
bioconductor featurerequest
updated 8.4 years ago by 21k • written 8.4 years ago by ▴ 60
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Pull request for customProDB package
customProDB featurerequest
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by ▴ 10
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[ChIPseeker; feature request] More flexibility in specifying the TSS region
ChIPseeker featurerequest tss
updated 9.9 years ago by ★ 1.2k • written 9.9 years ago by ▴ 40
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Feature Request: improve output when printing GenomicRanges instances
GenomicRanges featurerequest
10.4 years ago Keith Hughitt ▴ 180
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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 …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
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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