CTDPathSim2.0

R package CTDPathSim2.0 computes the similarity scores between patient tumor samples and cancer cell lines at genetic, genomic, and epigenetic levels integrating multi-omics datasets.

         It has five computational steps:
         
         Step 1. Computing sample-specific deconvoluted DNA methylation profile.
         
         Step 2. Computing sample-specific deconvoluted expression profile.
         
         Step 3: Computing sample and cell line-specific differentially expressed (DE) genes and biological pathways.
         
         Step 4: Computing sample and cell line-specific differentially methylated (DM) and differentially aberrated (DA) genes.
         
         Step 5: Computing sample-cell line pathway activity-based similarity score.

Installing the package

install.packages("remotes")

remotes::install_github("boseb/CTDPathSim2.0")

Check package vignette to run the tool

library(CTDPathSim2.0)

browseVignettes("CTDPathSim2.0")