https://github.com/jokergoo/rgreat

GREAT Analysis - Functional Enrichment on Genomic Regions
https://github.com/jokergoo/rgreat

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GREAT Analysis - Functional Enrichment on Genomic Regions

• Host: GitHub
• URL: https://github.com/jokergoo/rgreat
• Owner: jokergoo
• License: other
• Created: 2014-12-24T15:54:59.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2024-08-09T17:54:10.000Z (5 months ago)
• Last Synced: 2024-12-15T19:08:49.624Z (7 days ago)
• Language: R
• Homepage: https://jokergoo.github.io/rGREAT
• Size: 24.4 MB
• Stars: 85
• Watchers: 6
• Forks: 13
• Open Issues: 18
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS
  • License: LICENSE

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README

        
# GREAT Analysis - Functional Enrichment on Genomic Regions

[![R-CMD-check](https://github.com/jokergoo/rGREAT/workflows/R-CMD-check/badge.svg)](https://github.com/jokergoo/rGREAT/actions)

[![codecov](https://img.shields.io/codecov/c/github/jokergoo/rGREAT.svg)](https://codecov.io/github/jokergoo/rGREAT)

[![bioc](https://bioconductor.org/shields/downloads/devel/rGREAT.svg)](https://bioconductor.org/packages/stats/bioc/rGREAT/) 

[![bioc](http://www.bioconductor.org/shields/years-in-bioc/rGREAT.svg)](http://bioconductor.org/packages/devel/bioc/html/rGREAT.html)

**GREAT** ([Genomic Regions Enrichment of Annotations Tool](http://great.stanford.edu)) is a type of

functional enrichment analysis directly performed on genomic regions. This package 

implements the GREAT algorithm (the local GREAT analysis), also it supports directly 

interacting with the GREAT web service (the online GREAT analysis). Both analysis 

can be viewed by a Shiny application.

## Install

**rGREAT** is available on Bioconductor (http://bioconductor.org/packages/devel/bioc/html/rGREAT.html)

```r

if(!requireNamespace("BiocManager", quietly = TRUE)) {

    install.packages("BiocManager")

}

BiocManager::install("rGREAT")

```

If you want the latest version, install it directly from GitHub:

```r

library(devtools)

install_github("jokergoo/rGREAT")

```

## Citation

Zuguang Gu, et al., rGREAT: an R/Bioconductor package for functional enrichment on genomic regions. 

Bioinformatics, https://doi.org/10.1093/bioinformatics/btac745

## Online GREAT analysis

With online GREAT analysis, the input regions will be directly submitted to GREAT server, and the results

are automatically retrieved from GREAT server.

```r

set.seed(123)

gr = randomRegions(nr = 1000, genome = "hg19")

job = submitGreatJob(gr)

tbl = getEnrichmentTables(job)

```

## Local GREAT analysis

**rGREAT** also implements the GREAT algorithms locally and it can be seamlessly integrated

to the Bioconductor annotation ecosystem. This means, theoretically, with **rGREAT**, it is possible to perform GREAT analysis

with any organism and with any type of gene set collection / ontology

```r

res = great(gr, "MSigDB:H", "TxDb.Hsapiens.UCSC.hg19.knownGene")

tb = getEnrichmentTable(res)

```

To apply `great()` on other organisms, set the `biomart_dataset` argument:

```r

# giant panda

great(gr, "GO:BP", biomart_dataset = "amelanoleuca_gene_ensembl")

```

## License

MIT @ Zuguang Gu