I'm working through the Bioconductor book and am currently int he RNA-Seq statistics: R and Bioconductor section. I've actually used both R and Bioconductor before, but in Windows, not Linux.
I have R installed. If I try to run conda install r again, everything freezes up and I have to open up another window and sudo kill the process.
I did the following:
$ conda install -y bioconductor-deseq bioconductor-deseq2 bioconductor-edger r-gplots Fetching package metadata ................. Solving package specifications: . # All requested packages already installed. # packages in environment at /home/moltres/miniconda3/envs/bioinfo: # bioconductor-deseq 1.24.0 r3.3.2_0 bioconda bioconductor-deseq2 1.16.1 r3.3.2_0 bioconda bioconductor-edger 3.16.5 r3.3.2_0 bioconda r-gplots 2.17.0 r3.3.2_0 bioconda (bioinfo) $ curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r $ curl -O http://data.biostarhandbook.com/rnaseq/code/counts.txt $ cat counts.txt | Rscript deseq1.r 3x3 > results_deseq1.txt Error in library(DESeq) : there is no package called 'DESeq' Execution halted
So even though I just downloaded DESeq, it says I don't have the DESeq package. I did check my R version, and it's 3.4.3. I suspect that could be a problem, but I don't know how to change it in Linux. When I try doing everything in RStudio, I get a bunch of errors in dependencies and configuration upon using biocLite("DESeq").
Any ideas what's going wrong? I would appreciate any help.