Bioconductor HTSeqCounts

Showing : HTSeqCounts • reset

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deseq2 deseq edgeR rnaseq htseqcounts

7.9 years ago Deepali • 0

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2.5k

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edger htseqcounts

updated 8.0 years ago by Gordon Smyth 53k • written 8.0 years ago by Bioinformatics ▴ 30

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R summarizeoverlaps htseqcounts

updated 8.2 years ago by thokall ▴ 160 • written 8.2 years ago by Walter F. Baumann ▴ 10

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htseqcounts edger

updated 3.3 years ago by Randy • 0 • written 8.4 years ago by mictadlo ▴ 10

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4.0k

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edger htseqcounts

updated 8.4 years ago by Gordon Smyth 53k • written 8.4 years ago by mictadlo ▴ 10

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htseqcounts star rnaseq

8.4 years ago Ahdee ▴ 60

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featurecounts SAM htseqcounts

updated 2.5 years ago by Yang Liao ▴ 450 • written 8.7 years ago by courtney.stairs • 0

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chipseq deseq2 htseqcounts

updated 2.9 years ago by mhashan.j ▴ 10 • written 8.9 years ago by JunLVI ▴ 40

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edger htseqcounts rnaseq

updated 9.1 years ago by Aaron Lun ★ 29k • written 9.1 years ago by romsdahl • 0

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dexseq_count dexseq htseqcounts

9.3 years ago as1023 • 0

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deseq2 pca tximportdata htseqcounts

updated 9.5 years ago by Michael Love 43k • written 9.5 years ago by jarod_v6@libero.it ▴ 40

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deseq2 goseq htseqcounts rnaseq plant

updated 9.6 years ago by Gordon Smyth 53k • written 9.6 years ago by Ben Mansfeld • 0

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HTSeq HTSeqCounts Could not find function DEXSeq

updated 9.7 years ago by Martin Morgan 25k • written 9.7 years ago by sakura.nussbaum ▴ 10

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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

A: deseq2 - paired samples in 2 sequencing types with very different library sizes

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Popular Question to Lluís Revilla Sancho ▴ 760