‘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.
library(devtools)
install_github("seanchen607/deplink")
library(deplink)
source(system.file("script", "load_libs.R", package = "deplink"))
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:
[x] Chromatin modification
Genome instability
[x] Microsatellite instability (MSI)
Drug sensitivity
[x] Drug sensitivity from PRISM data set
Immune infiltration
[x] Immune signature gene (ISG)
Stemness
[x] Epithelial–mesenchymal transition (EMT)
Misc.
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:
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