https://github.com/mskilab-org/gGnome

R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
https://github.com/mskilab-org/gGnome

Last synced: 4 months ago
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R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework

• Host: GitHub
• URL: https://github.com/mskilab-org/gGnome
• Owner: mskilab-org
• License: mit
• Created: 2017-03-14T14:44:55.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-03-11T22:48:56.000Z (4 months ago)
• Last Synced: 2024-03-13T19:11:07.040Z (4 months ago)
• Language: R
• Homepage: http://mskilab.com/gGnome/tutorial.html
• Size: 87.8 MB
• Stars: 37
• Watchers: 9
• Forks: 19
• Open Issues: 12
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - gGnomes - genome-visualization/ggnomesr.png) (SV)

README

        
[![R-CMD-check](https://github.com/zining01/gGnome/actions/workflows/check-release.yaml/badge.svg)](https://github.com/zining01/gGnome/actions/workflows/check-release.yaml)

[![codecov.io](https://img.shields.io/codecov/c/github/mskilab/gGnome.svg)](https://codecov.io/github/mskilab/gGnome?branch=master)

# 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

```{r}

install.packages('devtools')

install.packages('testthat')

```

3. Install gGnome and dependent packages

```{r}

## allows dependencies that throw warnings to install

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)

devtools::install_github('mskilab/gGnome')

```

Documentation 

------------

[gGnome Tutorial](http://mskilab.com/gGnome/tutorial.html)

[alttext](https://github.com/mskilab/gGnome/articles/gGnome.png)

[PkgDown Site](https://tanubrata.github.io/gGnome/index.html)



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

------------

 

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