INCISOR

Identifying synethetic rescue interactions in humans.

Check out the manuscript in Molecular System Biology:

• msb website

System requirements

INCISOR has been tested on R versions >= 3.2. INCISOR has been tested on Linux and OS X.

Installation

First download the dataset from http://ds.dfci.harvard.edu/~asahu/pub.data/INCISOR/incisor.tar.gaz

The dataset could also be downloaded from dropbox.

The working directory (working dir) contains data directory containing the input data set.

Open R from INCISOR working directory

gunzip -c incisor.tar.gz|tar -xvf
mv incisor/data INCISOR-master/
cd INCISOR-master 
R

To run INCISOR, install dependencies

install.packages(c("Rcpp", "RcppArmadillo", "survival", "lsr", "doMC", "parallel", "data.table", "foreach", "effsize"))

Extra settings

In some environment to run the c-code following commands are required to set the variables :

Sys.setenv("PKG_CXXFLAGS"="-fopenmp")
Sys.setenv("PKG_LIBS"="-fopenmp")
library(RcppArmadillo)

Quick start

source("src/INCISOR.DU.top500.R")

"INCISOR.DU.top500.R" identifies top 500 SR interaction gene pairs. It runs all four screening steps (in-vitro, sof, clinical and phylogenetic screens). FDR level estimated on this subset will be obviously different from the full INCISOR. The final output is "positive.sr.du.interactions".

Screen all 500 million gene pair

Note the code takes 3 days in a 32 core machines

source("src/INCISOR.DU.R")

Results are available in "positive.sr.du.interactions"