Science Score: 23.0%
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
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.8%) to scientific vocabulary
Repository
R package for WebGestalt
Basic Info
- Host: GitHub
- Owner: bzhanglab
- Language: R
- Default Branch: master
- Homepage: https://bzhanglab.github.io/WebGestaltR/
- Size: 16.6 MB
Statistics
- Stars: 37
- Watchers: 5
- Forks: 13
- Open Issues: 16
- Releases: 1
Metadata Files
README.md
WebGestaltR
[!IMPORTANT] The new version of WebGestaltR requires Rust, which must be installed on your device prior to installing or updating the package from CRAN. See the installation section for more information.
WebGestalt R package is the R version of our well-known web application tool WebGestalt (www.webgestalt.org) that has on average 27,000 users from 140 countries and territories per year and has also been cited 371 in 2016. The advantage of this R package is that it can be easily integrated to other pipelines or simultaneously analyze multiple gene lists.
WebGestaltR function can perform popular enrichment analyses: ORA (Over-Representation Analysis), GSEA (Gene Set Enrichment Analysis) and NTA (Network Topology Analysis). Based on the user-uploaded gene list or gene list with scores (for GSEA method), WebGestaltR function will first map the gene list to entrez gene IDs and then summarize the gene list based on the GO (Gene Ontology) Slim data. After performing the enrichment analysis, WebGestaltR function also returns an user-friendly HTML report containing GO Slim summary and enrichment analysis result. If the functional categories have the DAG (directed acyclic graph) structure, the structure of the enriched categories can also be visualized in the report.
Installation
Requirements
- R (>= 4.0.0)
- Rust (>= 1.63.0)
Since WebGestaltR v1.0.0, Rust is used for core computations in the R package. Therefore, to install WebGestaltR, please download and install Rust from https://www.rust-lang.org/tools/install. For Mac, Linux, or Unix users, Rust can be installed from the command line, and Windows users can download a GUI installer. If using Windows: please make sure to install the GNU version of Rust. This will be an option when you run the installer.
Make sure you restart your terminal after installing Rust to ensure the Rust compiler is available in your path. You can check that Rust is installed correctly by running rustc --version in your terminal.
After installing Rust, you can install WebGestaltR by running the following command in an R session:
```R
install.packages("devtools") # run if devtools not already installed
devtools::install_github("bzhanglab/WebGestaltR") ```
During installation, the Rust compiler will be called to build the computation library used by WebGestaltR. If you run into problems with installation of the new version, please open a new issue.
Changes
[!NOTE] Besides the change in installation, there should be no difference in how the R package performs for existing use-cases. If you experience any difference in results that are not due to the data-update, that is considered a bug. Please report the changes you experience in a new issue.
WebGestaltR's core was re-written in Rust, which dramatically increased performance, with up to 15x the speed of previous versions. The new version also supports metabolomics, with support for 15 different ID types.
Owner
- Name: Zhang Lab
- Login: bzhanglab
- Kind: organization
- Location: Houston, TX
- Website: https://www.zhang-lab.org
- Repositories: 15
- Profile: https://github.com/bzhanglab
Translating omics data into biological insights.
GitHub Events
Total
- Issues event: 4
- Watch event: 1
- Delete event: 5
- Issue comment event: 7
- Push event: 15
- Pull request event: 10
- Fork event: 1
- Create event: 7
Last Year
- Issues event: 4
- Watch event: 1
- Delete event: 5
- Issue comment event: 7
- Push event: 15
- Pull request event: 10
- Fork event: 1
- Create event: 7
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Yuxing Liao | y****o@g****m | 221 |
| Yuxing Liao | e****1@g****m | 28 |
| Zhiao Shi | z****i@g****m | 16 |
| John Elizarraras | j****s@b****u | 4 |
| nfancy | 5****y | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 43
- Total pull requests: 25
- Average time to close issues: 4 months
- Average time to close pull requests: 3 days
- Total issue authors: 39
- Total pull request authors: 4
- Average comments per issue: 2.26
- Average comments per pull request: 0.56
- Merged pull requests: 21
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 11
- Average time to close issues: 4 months
- Average time to close pull requests: 19 minutes
- Issue authors: 5
- Pull request authors: 1
- Average comments per issue: 1.4
- Average comments per pull request: 0.09
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- shengqh (2)
- Pchaskar (2)
- njbowen (2)
- nfancy (2)
- iblacksand (2)
- nhu119 (1)
- wsjung (1)
- Nana-Liu-genetics (1)
- mglgc (1)
- ErickMUO (1)
- ecirri (1)
- corunesa85 (1)
- integratebio (1)
- imeMFK01 (1)
- rekren (1)
Pull Request Authors
- iblacksand (35)
- CGMossa (2)
- shengqh (1)
- nfancy (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- cran 407 last-month
- Total docker downloads: 185
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 3
(may contain duplicates) - Total versions: 16
- Total maintainers: 1
cran.r-project.org: WebGestaltR
Gene Set Analysis Toolkit WebGestaltR
- Homepage: https://github.com/bzhanglab/WebGestaltR
- Documentation: http://cran.r-project.org/web/packages/WebGestaltR/WebGestaltR.pdf
- License: LGPL-2 | LGPL-2.1 | LGPL-3 [expanded from: LGPL]
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Latest release: 0.4.6
published about 3 years ago
Rankings
Maintainers (1)
conda-forge.org: r-webgestaltr
- Homepage: https://github.com/bzhanglab/WebGestaltR
- License: LGPL-3.0-only
-
Latest release: 0.4.4
published almost 6 years ago
Rankings
Dependencies
- R >= 3.3 depends
- Rcpp * imports
- apcluster * imports
- doParallel >= 1.0.10 imports
- doRNG * imports
- dplyr * imports
- foreach >= 1.4.0 imports
- httr * imports
- igraph * imports
- jsonlite * imports
- methods * imports
- parallel >= 3.3.2 imports
- readr * imports
- rlang * imports
- svglite * imports
- whisker * imports