README.md

In bozdaglab/CTDPathSim2.0: Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

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")

bozdaglab/CTDPathSim2.0 documentation built on April 14, 2022, 12:39 a.m.