Science Score: 54.0%
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
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: plos.org -
✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
✓Institutional organization owner
Organization almaaslab has institutional domain (www.ntnu.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary
Keywords from Contributors
Repository
Efficient CSD implementation in R
Basic Info
- Host: GitHub
- Owner: AlmaasLab
- License: gpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://almaaslab.github.io/csdR
- Size: 1.74 MB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
csdR
This R-package implements the CSD algorithm presented by Voigt et al. 2017 in an efficient manner.
* Requrirements: Requirements: R (version 4.1.0 or higher) with packages WGCNA, optparse, glue, magrittr and Rcpp (and of course a C++ compiler) installed. Additionally, having an optimized Blas library such as openBlas is highly recommended for performance reasons (see this link for more info).
Installation
In order to install the release version from Bioconductor, do type in the R terminal:
if(!requireNamespace("BiocManager")){
install.packages("BiocManager")
}
BiocManager::install("csdR")
If you want to install the development version instead:
```
install.packages("devtools")
devtools::install_github("AlmaasLab/csdR", ref = "main") ```
Usage
Please see the package vignette. Additionally check out the article on csdR:
Pettersen, J.P., Almaas, E. csdR, an R package for differential co-expression analysis. BMC Bioinformatics 23, 79 (2022). https://doi.org/10.1186/s12859-022-04605-1
Issues and feedback
Please use the repository's issue tracker if you cannot make the package work or if you have suggestions for improvements.
Owner
- Name: AlmaasLab
- Login: AlmaasLab
- Kind: organization
- Email: eivind.almaas@ntnu.no
- Location: Trondheim, Norway
- Website: http://www.ntnu.edu/almaaslab
- Repositories: 4
- Profile: https://github.com/AlmaasLab
Network Systems Biology
GitHub Events
Total
- Issues event: 3
- Watch event: 1
- Push event: 8
Last Year
- Issues event: 3
- Watch event: 1
- Push event: 8
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jakob Peder Pettersen | j****n@g****m | 34 |
| Nitesh Turaga | n****a@g****m | 4 |
| J Wokaty | j****y@s****u | 2 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 6,295 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: csdR
Differential gene co-expression
- Homepage: https://almaaslab.github.io/csdR https://github.com/AlmaasLab/csdR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/csdR/inst/doc/csdR.pdf
- License: GPL-3
-
Latest release: 1.14.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1.0 depends
- Rcpp * imports
- RhpcBLASctl * imports
- WGCNA * imports
- glue * imports
- matrixStats * imports
- BiocStyle * suggests
- dplyr * suggests
- igraph * suggests
- knitr * suggests
- magrittr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite