Section outline

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    R and Transcriptomics Analysis

    24 May 2023 (streamed)

    For any assistance, please contact frederic.schutz@sib.swiss

  • Material

    Course material will be put online before the course.

    • Practical 1: RNA-seq analysis

      We are going to analyze an RNA-seq dataset which can be found in EBI Expression Atlas (GXA). Dataset E-GEOD-50760 was published in the paper A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients, published in "Molecular Oncology".

      The dataset contains 54 samples from 18 individuals. For each individual, three samples have been collected: a primary colorectal cancer sample, a metastatic liver sample, and a normal sample of the surrounding colonic epithilium.

      The files provided contain raw readcounts, as well as the details of the information associated with each sample.

      In order to analyze these samples, we will use DEseq2 in the way we worked during the RNA-seq course; however, the final analysis will be a bit more complex, as we will need to take into account the individuals into the analysis. You can start by reproducing an analysis similar to what we did in the course, and we will discuss the more advanced parts later.