README.md

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

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 Funding sources ------------ ```

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.