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.
install.packages("remotes")
remotes::install_github("boseb/CTDPathSim2.0")
library(CTDPathSim2.0)
browseVignettes("CTDPathSim2.0")