Preprint - Version 1

[Preprint] - Version 1

This is the first release of the transportome profiler analysis. A synopsis from the readme is below:

This repository contains the code for the analysis on the expression profile of the transportome in Cancer based on the MTP-DB.

Read the preprint here: Profiling the Expression of Transportome Genes in cancer: A systematic approach

This is a two-step process. The database is queried for information by the script in src/geneset_maker. The algorithm generates gene sets ready for use by GSEA. We then generate a series of DEG tables with src/run_dea based on the comparison of gene expression from TCGA (cancer) and GTEx (healthy) tissues.
Finally, GSEA is called by src/gsea_runner in a pre-ranked manner on all the DEG tables with all of the genesets, making enrichment tables. The enrichment tables are then processed by a script in src/gsea_runner to make enrichment plots.