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functions
functions
 
 
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pipelines
 
 
scripts
scripts
 
 
README.md
README.md
 
 
master.sh
master.sh
 
 

README.md

Code organisation

functions

This folder hosts the code for R and python packages that were developed for this project as well as links to external tools. In short,

  • rprism R package with useful functions for reading, writing, and manipulating data tables of the project as well as performing tasks repeated in many analyses such as computation of pvalues and multiple testing correction.

  • rprismtools R package with useful functions for drawing figures.

  • pyprism Python package with useful functions for reading, writing, and manipulating data tables of the project. It provides python implementations for many of the functions available in rprism.

  • pyprismtools Python package with useful functions for drawing figures.

  • tools See README files of the linked submodules.

Contributors

pipelines

This folder hosts the bioinformatics pipelines that were developed or edit from existing pipelines in order to run all bioinformatics analyses for the project. In short,

  • kallisto_tximport a Snakemake port of RNASeq_pipeline by gevaertlab. Command line were duplicated as-is, additional logging files were added to follow the pipeline's execution cautiously. See pipelines/kallisto_tximport/README.md for more details.

  • rnafusion clone of the nf-core rnafusion pipeline v1.2.0. See pipelines/rnafusion/README.md for more details.

  • wes a Snakemake pipeline developed specifically for the project. It performs a comprehensive analysis of WES data in order to identify, filter, and annotate germline mutations, somatic mutations, copy-number alterations, purity and ploidy, and microsatellite instability in each pair of tumor/normal. It may also run in tumor-only mode for almost all analyses except microsatellite instability. See pipelines/wes/README.md for more details.

Contributors

scripts

This folder gather all the scripts that were used to perform the analysis, extract the numbers, and draw the figures that underlie the paper. Each analysis is organised in a subfolder using a structure similar to that of the pipelines/wes pipeline. The code is organized and made easily runnable through Snakemake. See scripts/README.md for more details.

Contributors