Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
6 of 22 committers (27.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.7%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Gene set variation analysis
Statistics
- Stars: 224
- Watchers: 9
- Forks: 42
- Open Issues: 11
- Releases: 0
Topics
Metadata Files
README.md
GSVA: gene set variation analysis for microarray and RNA-seq data
Current Bioconductor build status
- release 
- development 
The GSVA package allows one to perform a change in coordinate systems of molecular measurements, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods such as functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. For citing GSVA as a software package, please use the following reference:
Hänzelmann S., Castelo R. and Guinney J. GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013.
Installation
This is the development version of the R/Bioconductor package GSVA. This version is unstable and should be used only to test new features. If you are looking for the release version of this package please go to its package release landing page at https://bioconductor.org/packages/GSVA and follow the instructions there to install it.
If you were really looking for this development version, then to install it you need first to install the development version of Bioconductor and then type the following line from the R shell:
r
BiocManager::install("GSVA", version = "devel")
Alternatively, you can install it from GitHub using the remotes package.
r
install.packages("remotes")
library(remotes)
install_github("rcastelo/GSVA")
Questions, bug reports and issues
For questions and bug reports regarding the release version of GSVA please use the Bioconductor support site. For feature requests or bug reports and issues regarding this development version of GSVA please use the GitHub issues tab at the top-left of this page.
Contributing
Contributions to the software codebase of GSVA are welcome as long as contributors abide to the terms of the Bioconductor Contributor Code of Conduct. If you want to contribute to the development of GSVA please open an issue to start discussing your suggestion or, in case of a bugfix or a straightforward feature, directly a pull request.
Funding
This software project was supported in part by the Essential Open Source Software for Science (EOSS) program at Chan Zuckerberg Initiative, and the Spanish Ministry of Science, Innovation and Universities.
Owner
- Name: Robert Castelo
- Login: rcastelo
- Kind: user
- Location: Barcelona
- Company: Universitat Pompeu Fabra
- Website: https://functionalgenomics.upf.edu
- Twitter: robertclab
- Repositories: 15
- Profile: https://github.com/rcastelo
biostatistics, machine learning, genetics, genomics, R/Bioconductor
GitHub Events
Total
- Issues event: 46
- Watch event: 24
- Delete event: 12
- Issue comment event: 41
- Push event: 100
- Pull request event: 31
- Fork event: 4
- Create event: 12
Last Year
- Issues event: 46
- Watch event: 24
- Delete event: 12
- Issue comment event: 41
- Push event: 100
- Pull request event: 31
- Fork event: 4
- Create event: 12
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Robert Castelo | r****o@u****u | 201 |
| Axel Klenk | a****k@g****m | 99 |
| pablo-rodr-bio2 | p****2@g****m | 72 |
| Dan Tenenbaum | d****a@f****g | 27 |
| [rcastelo] | [****o@u****] | 24 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| peremoles | p****s@g****m | 9 |
| Herve Pages | h****s@f****g | 6 |
| Aaron | a****9@g****m | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****a@g****m | 2 |
| Alexey Sergushichev | a****x@g****m | 2 |
| A Wokaty | a****y@s****u | 2 |
| Chao-Jen Wong | c****2@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| JoanFernandez | j****1@g****m | 1 |
| Benilton Carvalho | b****h@j****u | 1 |
| pablo-rodr-bio2 | p****o@g****m | 1 |
| liripo | l****o@q****m | 1 |
| Qian Liu | q****7@b****u | 1 |
| Paul Shannon | p****n@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 129
- Total pull requests: 91
- Average time to close issues: about 2 months
- Average time to close pull requests: 2 days
- Total issue authors: 86
- Total pull request authors: 8
- Average comments per issue: 1.93
- Average comments per pull request: 0.09
- Merged pull requests: 80
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 30
- Pull requests: 31
- Average time to close issues: 22 days
- Average time to close pull requests: about 17 hours
- Issue authors: 17
- Pull request authors: 3
- Average comments per issue: 1.03
- Average comments per pull request: 0.0
- Merged pull requests: 29
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rcastelo (24)
- axelklenk (14)
- Chrisdoan9 (3)
- abadgerw (3)
- FADHLyemen (2)
- YouriTasse (2)
- andreyurch (2)
- kaqisekuzi (1)
- llrs (1)
- toddcreasy (1)
- sup27606 (1)
- Chamberlain1993 (1)
- Zhixuan-Jing (1)
- bbimber (1)
- OnlyBelter (1)
Pull Request Authors
- axelklenk (40)
- pablo-rodr-bio2 (27)
- rcastelo (14)
- peremoles (6)
- aabaker99 (1)
- assaron (1)
- Liripo (1)
- JoanFernandez (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 582,024 total
- Total dependent packages: 15
- Total dependent repositories: 0
- Total versions: 14
- Total maintainers: 1
bioconductor.org: GSVA
Gene Set Variation Analysis for Microarray and RNA-Seq Data
- Homepage: https://github.com/rcastelo/GSVA
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.pdf
- License: GPL (>= 2)
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Latest release: 2.2.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.5.0 depends
- Biobase * imports
- BiocParallel * imports
- BiocSingular * imports
- DelayedArray * imports
- DelayedMatrixStats * imports
- GSEABase * imports
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- graphics * imports
- methods * imports
- parallel * imports
- sparseMatrixStats * imports
- stats * imports
- utils * imports
- BiocGenerics * suggests
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- RColorBrewer * suggests
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