regsplice
R package for detection of differential exon usage in RNA-seq and exon microarray data
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
1 of 10 committers (10.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.2%) to scientific vocabulary
Keywords from Contributors
Repository
R package for detection of differential exon usage in RNA-seq and exon microarray data
Basic Info
Statistics
- Stars: 3
- Watchers: 4
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
regsplice
This repository contains the development version of the R package regsplice.
The release version is available from Bioconductor.
The regsplice package implements statistical methods for the detection of differential exon usage (differential splicing) in RNA sequencing (RNA-seq) and exon microarray data sets. The regsplice methods are based on the use of the lasso (L1-regularization) to improve the power of standard generalized linear models. A key advantage is that runtimes are fast compared to other leading approaches.
A paper describing the statistical methodology and performance comparisons with other methods is currently in preparation.
Install release version
The release version can be installed from Bioconductor using the Bioconductor installer. This will also install all required dependencies. This is the recommended option for most users.
{r}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("regsplice")
Install development version
The development version can be installed from this GitHub repository using devtools::install_github.
{r}
install.packages("devtools")
library(devtools)
install_github("lmweber/regsplice")
Alternatively, the development version can also be installed using the "Devel" version of Bioconductor (see Bioconductor documentation for details). However, the Bioconductor Devel version may sometimes be a few days behind the GitHub version.
Dependencies
The regsplice package depends on:
glmnet,pbapply(from CRAN)limma,edgeR,SummarizedExperiment(from Bioconductor)
If you install using the Bioconductor installer, all dependencies will be installed automatically.
If you install from GitHub, the Bioconductor dependencies need to be installed separately.
{r}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install(c("limma", "edgeR", "SummarizedExperiment"))
Owner
- Name: Lukas Weber
- Login: lmweber
- Kind: user
- Location: Boston, MA
- Company: Boston University
- Website: https://lmweber.org/
- Repositories: 75
- Profile: https://github.com/lmweber
Assistant Professor, Department of Biostatistics, Boston University
GitHub Events
Total
Last Year
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lukas M Weber | l****r@g****m | 176 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 6 |
| Herve Pages | h****s@f****g | 4 |
| vobencha | v****a@g****m | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| Martin Morgan | m****n@f****g | 2 |
| LiNk-NY | m****9@g****m | 1 |
| Kayla-Morrell | k****l@r****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 13,983 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: regsplice
L1-regularization based methods for detection of differential splicing
- Homepage: https://github.com/lmweber/regsplice
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/regsplice/inst/doc/regsplice.pdf
- License: MIT + file LICENSE
-
Latest release: 1.34.1
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- S4Vectors * imports
- SummarizedExperiment * imports
- edgeR * imports
- glmnet * imports
- limma * imports
- methods * imports
- pbapply * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests