7. Extracting differentially expressed genes with edgeR¶

To set up R¶

We will install one package manually, so R knows where to install some more:

module load R
R
install.packages("sp")
y
y
57
q()
n

Run this edgeR script (nema.salmon.R) that loads all this. For more information, see the edgeR manual

curl -O -L https://raw.githubusercontent.com/humberto-ortiz/khmer-protocols/escambron/mrnaseq/nema.salmon.R
Rscript nema.salmon.R

These will produce two plots, nema-edgeR-MDS.pdf and nema-edgeR-MA-plot.pdf.

You can see the plot outputs for the whole data set (all the reads) here:

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