a. We provide a Snakemake implementation of the pipeline to perform TITAN analysis starting from BAM files to TitanCNA results. Please see snakemake/ for more details.
b. R scripts for running TitanCNA analysis
The R_scripts directory contains the actual R script to run the (R component of the) TitanCNA analysis as well as an R script to select the optimal solution.
While the Snakemake pipeline will make use of R script within R_scripts, you can learn about more details of the R script here R_scripts/.
The Snakemake workflow is in another Git repo: https://github.com/gavinha/TitanCNA_10X_snakemake