README.md

In bitmask/NEMpipeline: Pipeline to run various NEM and non-NEM methods on simulated and 2 experimental datasets

NEM Pipeline

To generate simulated data with false positive and false negative rates as specified, run methods, and plot results. Results will be written into the directory specified.

Installation

devtools::install_github("bitmask/labnetmet")
devtools::install_github("bitmask/NEMpipeline")

Optional dependencies:

lem: install.packages("https://www.mimuw.edu.pl/~szczurek/lem/lem_1.0.tar.gz",repos=NULL, type="source")
bnem: devtools::install_github("MartinFXP/B-NEM")
pcnem: devtools::install_github("cbg-ethz/pcNEM")
fgnem: https://sysbio.soe.ucsc.edu/projects/fgnem/

Usage

library(NEMpipeline)
set.seed(42)
alpha <- 0.15
beta <- 0.05
output_dir <- "~/projects/NEMpipelineoutput" # directory to write data and plots to
run_simulated_pipeline(alpha, beta, output_dir)

bitmask/NEMpipeline documentation built on Jan. 30, 2020, 12:42 p.m.