R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
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DESCRIPTION
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README.md

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gGnome

The gGnome package provides a flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in the R6 object oriented standard and built around a powerful GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges.

Install

  1. Install dependent packages and latest Bioconductor (if you haven't already)
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
install.packages('devtools')
install.packages('testthat')
  1. Install dependent mskilab R packages
devtools::install_github('mskilab/gUtils')
devtools::install_github('mskilab/gTrack')
  1. Install gGnome
devtools::install_github('mskilab/gGnome)

Documentation

gGnome Tutorial

alttext

Attributions

Marcin Imielinski - Assistant Professor, Weill Cornell Medicine Core Member, New York Genome Center.

Xiaotong Yao - Graduate Research Assistant, Weill Cornell Medicine, New York Genome Center.

Joseph DeRose - Undergraduate Research Assistant, New York Genome Center.

Rick Mortensen - Undergraduate Research Assistant, New York Genome Center, Memorial Sloan-Kettering Cancer Center

Funding sources