Science Score: 49.0%
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Found 2 DOI reference(s) in README -
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Repository
GREAT Analysis - Functional Enrichment on Genomic Regions
Basic Info
- Host: GitHub
- Owner: jokergoo
- License: other
- Language: R
- Default Branch: master
- Homepage: https://jokergoo.github.io/rGREAT
- Size: 24.5 MB
Statistics
- Stars: 90
- Watchers: 5
- Forks: 13
- Open Issues: 20
- Releases: 0
Metadata Files
README.md
GREAT Analysis - Functional Enrichment on Genomic Regions
GREAT (Genomic Regions Enrichment of Annotations Tool) 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", biomartdataset = "amelanoleucagene_ensembl") ```
License
MIT @ Zuguang Gu
Owner
- Name: Zuguang Gu
- Login: jokergoo
- Kind: user
- Location: Heidelberg, Germany
- Company: German Cancer Research Center
- Website: http://jokergoo.github.io
- Repositories: 28
- Profile: https://github.com/jokergoo
A bioinformagician
GitHub Events
Total
- Issues event: 3
- Watch event: 4
- Issue comment event: 2
Last Year
- Issues event: 3
- Watch event: 4
- Issue comment event: 2
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zuguang Gu | j****o@g****m | 167 |
| Zuguang Gu | z****u@d****e | 32 |
| z.gu | z****u@b****8 | 17 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 9 |
| Dan Tenenbaum | d****a@f****g | 8 |
| Nick Semenkovich | n****k@s****m | 4 |
| Herve Pages | h****s@f****g | 4 |
| andvon | v****a@g****m | 3 |
| vobencha | v****n@r****g | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****a@g****m | 2 |
| d.tenenbaum | d****m@b****8 | 2 |
| Bioconductor Git-SVN Bridge | b****c@b****g | 2 |
| LiNk-NY | m****9@g****m | 1 |
| s.arora | s****a@b****8 | 1 |
| Sonali Arora | s****a@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 56
- Total pull requests: 2
- Average time to close issues: 2 months
- Average time to close pull requests: 4 months
- Total issue authors: 42
- Total pull request authors: 2
- Average comments per issue: 2.55
- Average comments per pull request: 2.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 7 months
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 2.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jokergoo (6)
- peranti (4)
- semenko (4)
- wbvguo (2)
- dktanwar (2)
- Pickledzebra (2)
- ilibarra (1)
- jiayiliujiayi (1)
- dougbarrows (1)
- Dragonlongzhilin (1)
- dgodovich (1)
- coolleen516 (1)
- zqzneptune (1)
- ashishjain1988 (1)
- skpeterson (1)
Pull Request Authors
- andvon (2)
- semenko (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 65,966 total
- Total dependent packages: 3
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: rGREAT
GREAT Analysis - Functional Enrichment on Genomic Regions
- Homepage: https://github.com/jokergoo/rGREAT http://great.stanford.edu/public/html/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/rGREAT/inst/doc/rGREAT.pdf
- License: MIT + file LICENSE
-
Latest release: 2.10.0
published 10 months ago