README.md

In acranej/InProgress: Need a name

InProgress Overview

This pacakge is designed to take MANTA or SvABA VCF files which have been run without a paired normal and classify each rearrangement as germline or somatic.

System Requirements and Dependencies

• This has been tested on the current versions of OSX, Linux, Ubuntu, Windows (as of April 1, 2022)

Installation

1. Install R-4.0 or newer (https://www.r-project.org/)
2. Install necessary packages ```{r} install.pacakges('devtools') install.packages('parallel') install.packages('BiocManager')

library(BiocManager) BiocManager::install('GenomicRanges')

library(devtools) devtools::install_github('mskilab/gUtils') ``` Documentation for these packages can be found at: \ devtools \ parallel \ BiocManager \ GenomicRanges \ gUtils

1. Install InProgress

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE) 
devtools::install_github('acranej/InProgress')

acranej/InProgress documentation built on April 25, 2022, 5:30 a.m.