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
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○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
4 of 10 committers (40.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.7%) to scientific vocabulary
Last synced: 10 months ago
·
JSON representation
Repository
R package for Time-course Gene Set Analysis
Basic Info
- Host: GitHub
- Owner: sistm
- License: gpl-2.0
- Language: R
- Default Branch: master
- Homepage: http://sistm.github.io/TcGSA/
- Size: 8.72 MB
Statistics
- Stars: 6
- Watchers: 3
- Forks: 2
- Open Issues: 2
- Releases: 0
Created about 12 years ago
· Last pushed 12 months ago
Metadata Files
Readme
License
README.Rmd
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# `TcGSA`
[](https://cran.r-project.org/package=TcGSA)
[](https://github.com/sistm/TcGSA/actions/workflows/R-CMD-check.yaml)
[](https://www.r-pkg.org/pkg/TcGSA)
## Overview
`TcGSA` is a package which performs *Time-course Gene Set Analysis* from **microarray data**, and provide nice representations of its results.
On top of the CRAN help pdf-file, the following article explains what TcGSA is about:
>Hejblum, BP, Skinner, J, & Thiébaut, R (2015). Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. *PLOS Computational Biology*, **11**(6):e1004310. [](https://doi.org/10.1371/journal.pcbi.1004310)
## Installation
TcGSA imports the `multtest` package which is not available on [CRAN](https://cran.r-project.org/), but is available on the [Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/multtest.html) repository.
Before installing TcGSA, be sure to have this `multtest` package installed. If not, you can do so by running the following:
```{r bioc-install, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("multtest")
```
The easiest way to get `TcGSA` is to install it from [CRAN](https://cran.r-project.org/package=TcGSA):
```{r CRAN-install, eval=FALSE}
install.packages("TcGSA")
```
or to get the development version from [GitHub](https://github.com/sistm/TcGSA/):
```{r GitHub-install, eval=FALSE}
#install.packages("devtools")
devtools::install_github("sistm/TcGSA")
```
## Microarrays vs RNA-seq
`TcGSA` relies on a Gaussian assumption for the expression data, which is suitable for
normalized microarray data. Due to their count and heteroskedastic nature, RNA-seq
data need to be handled differently and ***TcGSA cannot deal with RNA-seq data***.
For RNA-seq data, please have a look at the [Bioconductor package `dearseq`](https://bioconductor.org/packages/dearseq/)
which incorporates similar functionalities for analyzing RNA-seq data.
-- Boris Hejblum
Owner
- Name: SISTM
- Login: sistm
- Kind: organization
- Location: Bordeaux, france
- Website: https://team.inria.fr/sistm/
- Repositories: 17
- Profile: https://github.com/sistm
research team from Inserm BPH U1219 & Inria BSO
GitHub Events
Total
- Watch event: 3
- Push event: 21
Last Year
- Watch event: 3
- Push event: 21
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Boris | b****i@g****m | 90 |
| Boris Hejblum | b****m@i****m | 35 |
| borishejblum | b****h@g****m | 31 |
| borishejblum | b****m@i****r | 27 |
| borishejblum | b****m@u****r | 24 |
| damienchimits | d****s@g****m | 5 |
| borishejblum | b****m@s****u | 5 |
| borishejblum | b****h@g****m | 3 |
| Boris | B****s@m****l | 2 |
| anthonydevaux | 3****x | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 15
- Total pull requests: 9
- Average time to close issues: 4 months
- Average time to close pull requests: 17 days
- Total issue authors: 13
- Total pull request authors: 3
- Average comments per issue: 3.6
- Average comments per pull request: 0.11
- Merged pull requests: 6
- 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
- PFRoux (2)
- mimisikai (2)
- jcfoo (1)
- friedue (1)
- stuomiva (1)
- ShuyiGan (1)
- Biofarmer (1)
- elcega (1)
- dzhakparov (1)
- mchimenti (1)
- mebbert (1)
- emilyleventhal (1)
- saraa30 (1)
Pull Request Authors
- damienchimits (6)
- borishejblum (2)
- anthonydevaux (1)
Top Labels
Issue Labels
help wanted (5)
question (3)
bug (2)
enhancement (2)
Pull Request Labels
enhancement (1)
Packages
- Total packages: 1
-
Total downloads:
- cran 330 last-month
- Total docker downloads: 21,613
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 9
- Total maintainers: 1
cran.r-project.org: TcGSA
Time-Course Gene Set Analysis
- Homepage: http://sistm.github.io/TcGSA/
- Documentation: http://cran.r-project.org/web/packages/TcGSA/TcGSA.pdf
- License: GPL-2 | file LICENSE
-
Latest release: 0.12.13
published 12 months ago
Rankings
Forks count: 17.8%
Stargazers count: 24.2%
Dependent packages count: 29.8%
Average: 31.5%
Dependent repos count: 35.5%
Downloads: 50.4%
Maintainers (1)
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.0.2 depends
- ggplot2 >= 2.0.0 depends
- GSA * imports
- cluster * imports
- cowplot * imports
- grDevices * imports
- graphics * imports
- gtools * imports
- lme4 >= 1.0 imports
- multtest * imports
- reshape2 * imports
- splines * imports
- stats * imports
- stringr * imports
- utils * imports
- BiocManager * suggests
- GEOquery * suggests
- dearseq * suggests
- doParallel * suggests
- foreach * suggests
- knitr * suggests
- parallel * suggests
- rmarkdown * suggests