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  • 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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  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

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