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README.md
# 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 rGREAT: an R/Bioconductor package for functional enrichment on genomic regions Zuguang Gu, Daniel H├╝bschmann Bioinformatics, btac745, 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") ``` For more details, please go to [the package vignettes](https://jokergoo.github.io/rGREAT/). ## License MIT @ Zuguang Gu