hello,
I have 9 experiments (human RNAseq data (control/treatment)),I did RNAseq analysis by CLC genomics,now I want to do differential expression between 2 condition(control/treatment) by R.I need DE for all treated vs all controls samples (I mean I do not want DE for each experiment separately). is there any R package?
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Edalat •
DESeq2 is what you are looking for. Here you can find both the vignette and the example R script. Also I havent used CLC genomics; do you have the count data? If not, use another R package see here to get your counts and use DESeq2 afterwards. As long as you arrange the condition part well, you can put as many samples you want
See this article, it may help.
https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq/inst/doc/DESeq.pdf
Preferably refer to the newest version: https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf
Sure, but the article from 2016 considers old version, DESeq... When DESeq2 is from 2014, isn't it?
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