/deplink

Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)

Primary LanguageR

deplink

an R package to compare the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)

Project Status: Active - The project has reached a stable, usable state and is being actively developed.

‘deplink’ compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature).

Data source: DepMap (release 2019q4) and CCLE

For details, please see Tutorial.

⚙️ Install deplink in R (>= 3.5.0)

library(devtools)
install_github("seanchen607/deplink")

⏳ Load deplink and data libraries

library(deplink)
source(system.file("script", "load_libs.R", package = "deplink"))

🧬 Usage

For example, deplink compares the genetic/epigenetic features between cancer cell lines with highest and lowest dependencies of "9-1-1" complex members:

deplink(signature.name = "9-1-1", signature = c("RAD9A", "RAD1", "HUS1", "RAD17"))

The results will be output to a local directory (default: root directory) under a folder in name of the designated "signature.name" ("9-1-1" in this case).

Several cutoffs are set by default as below and can be changed by will. Please see the help page for more details (?deplink).

cutoff.freq        = 10
cutoff.percentile  = 0.2
cutoff.pvalue      = 0.05
cutoff.qvalue      = 0.1
cutoff.diff        = 0.1
cutoff.fc          = 2

The comparison covers the following features:

  • Genomic/epigenetic features

    • Genetic dependency
    • Gene expression
    • Chromatin modification

  • Genome instability

    • Genetic mutation
    • COSMIC signature
    • Tumor mutation burden (TMB)
    • Copy number variation (CNV)
    • Microsatellite instability (MSI)

  • Drug sensitivity

    • Drug sensitivity from GDSC data set
    • Drug sensitivity from PRISM data set

  • Immune infiltration

    • Immune signature gene (ISG)

  • Stemness

    • mRNA stemness index (mRNAsi)
    • Epithelial–mesenchymal transition (EMT)

  • Misc.

    • Cancer type
    • Hallmark signature

✏️ Authors

Xiao CHEN, PhD

Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York

https://www.researchgate.net/profile/Xiao_Chen126

If you use deplink in published research, please cite the most appropriate paper(s) from this list:

  1. X Chen, J McGuire, F Zhu, X Xu, Y Li, D Karagiannis, R Dalla-Favera, A Ciccia, J Amengual & C Lu (2020). Harnessing genetic dependency correlation network to reveal chromatin vulnerability in cancer. In preparation.