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-   -   Windows Ubuntu, Kallisto, R, sleuth, conda, bioconda, miniconda, bioconductor (http://seqanswers.com/forums/showthread.php?t=94290)

seqtechno1 05-06-2020 10:01 AM

Windows Ubuntu, Kallisto, R, sleuth, conda, bioconda, miniconda, bioconductor
 
Hello everyone,

I'm trying to sort out getting sleuth working with R. I currently have windows ubuntu subshell running and have installed conda, bioconda, bioconductor, R, kallisto, and sleuth. I'm very confused about the nature of package managers how to keep everything straight between them. Right Kallisto is installed properly and I have generated the abundances.tsv file using one sample paired end reads and the index file I opted to download instead of generate myself. Now I am ready for downstream analysis using the abundances.tsv in sleuth, which was written to work with R. I have installed R and can enter the R prompt via ubuntu. I'm having trouble installing devtools for R / bioconductor and I cannot get sleuth to run properly, I suspect it is something to do with having one too many coding language packages / dependencies and something got convoluted or crossed somewhere. Any advice?

SeqTechno


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