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edgeR rpkm source code

updated 6.7 years ago by Martin Morgan 25k • written 6.7 years ago by thibault.lorin ▴ 10

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goseq DESEQ2 RSTUDIO CODE

updated 6.1 years ago by Steve Lianoglou 13k • written 6.1 years ago by amyfm ▴ 10

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r code rna wobble

3.8 years ago fawazfebin ▴ 30

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Coc code conduct Bioconductor News

14 months ago Laurent Gatto 1.5k

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Comment: tximport from Galaxy output by Pragathi • 0

@mikelove :Thank u

Comment: Can I use VST on TPM data? (DESeq2) by Michael Love 35k

The DESeq2 VST in `vst()` doesn't make sense on TPM because it is designed for NB distributed count data. The TPM are not close to NB (nega…

Comment: Can I use VST on TPM data? (DESeq2) by Bumble • 0

Hello again, Thank you very much for your reply. I had used rlog on the count data and got a good grouping on the sample heat map and an al…

Comment: Plot normalized expression or count values for a specific gene in limma by bioinformaticssrm2011 • 0

I am trying to use the same plot, but **norm** here is a count table where rows are gene name and column is a sample, how "**grouping**" fa…

Comment: tximport from Galaxy output by Michael Love 35k

See the tximport vignette, it explains all of this. I can't provide support for Galaxy here.

Votes

C: about paired-samples in edgeR

A: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e

Answer: Error with hclust

Filtering of RNA-seq data in EdgeR

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