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CCBR / Pipeliner

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
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Use msigdb for pathway analysis; perform additional analysis on specific db/pathway #474

Open slsevilla opened 1 year ago

slsevilla commented 1 year ago

Utilizing Pipeliner output, perform pathway analysis in two ways:

  1. Pathway analysis msigdb - Performs GSEA and/or ORA analysis using msigdb with Pipeiner direct output. Should be able to intake db list with C1, and C2, and H sub-types. Output heatmaps, interactive DT, ridgeplot
  2. Pathway analysis extension - Performs Step #1 if this hasn't been performed, and given a specific datasbase / pathway input will create pathway specific heatmaps for signficant genes, presents all genes that passed filtering present in pathway in a DT, and creates GSEA plot.
slsevilla commented 1 year ago

scripts have been created and stored here: /data/CCBR_Pipeliner/sandbox/pathway_scripts