Transportome Profiler - Final Release 3

We noticed that the barplots had different results than the UpSet plots - this was due from the fact thay they used two different sources for their data. Now, the barplots use the same data as the UpSet plots, making them identical.

Attached result data and replay package can be found on Zenodo: https://zenodo.org/records/16355310

Transportome Profiler - Final Release 2

We noticed some issues with one of the plots, this release fixes it.

Results are here: https://zenodo.org/records/15656739

Transportome Profiler - Final Release 1

This is the final release of Transportome Profiler.

The replay package and results can be found on Zenodo: https://doi.org/10.5281/zenodo.15281114
The Docker container can be found on Docker Hub: https://hub.docker.com/layers/cmalabscience/transportome_profiler_env/1/images/sha256-4313bd6e107ca475fde23eacc2a4f078912a550f599783b8bc0dea2ba56123de

Transportome Profiler V2 - Prerelease 2

This pre-release adds some extra plots and fixes a variety of minor issues in the plots.

Transportome Profiler V2 - Prerelease 1

This is a pre-release of the analysis. It uses the MTP-DB Version 1.25.04.

All metrics are computed for all samples and attached as binaries.

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.