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

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gGnome

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R API for genome graphs

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 R-3.6 or up

  2. Install devtools

install.packages('devtools')
install.packages('testthat')
  1. Install gGnome and dependent packages
## allows dependencies that throw warnings to install
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)


devtools::install_github('mskilab/gGnome')

Documentation

gGnome Tutorial

alttext

PkgDown Site

Attributions

Marcin Imieliński - Associate Professor, Weill Cornell Medicine Core Member, New York Genome Center.

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

Zi-Ning Choo - Graduate Research Assistant, Weill Cornell Medicine, New York Genome Center.

Alon Shaiber - Genomics Data Scientist, Weill Cornell Medicine, New York Genome Center.

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

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

Max Chao - Bioinformatic Analyst, Weill Cornell Medicine, New York Genome Center

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

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