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gemma.R

An R wrapper for the Gemma RESTful API

https://github.com/pavlidislab/gemma.r

Science Score: 57.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 11 committers (36.4%) from academic institutions
  • ✓
    Institutional organization owner
    Organization pavlidislab has institutional domain (pavlab.msl.ubc.ca)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary

Keywords

bioinformatics gemma genomics transcriptomics

Keywords from Contributors

bioconductor-package gene grna-sequence immune-repertoire ontology
Last synced: 6 months ago · JSON representation

Repository

An R wrapper for the Gemma RESTful API

Basic Info
Statistics
  • Stars: 10
  • Watchers: 1
  • Forks: 1
  • Open Issues: 9
  • Releases: 2
Topics
bioinformatics gemma genomics transcriptomics
Created about 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# gemma.R: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses 


[![R build status](https://github.com/PavlidisLab/gemma.R/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/PavlidisLab/gemma.R/actions)
[![Codecov test coverage](https://codecov.io/gh/PavlidisLab/gemma.R/branch/master/graph/badge.svg)](https://codecov.io/gh/PavlidisLab/gemma.R?branch=master)
[![DOI](https://img.shields.io/badge/doi-10.1093/database/baab006-yellow.svg)](https://doi.org/10.1093/database/baab006)


This is an R wrapper for [Gemma](http://gemma.msl.ubc.ca)’s RESTful [API](https://gemma.msl.ubc.ca/rest/v2/). Gemma is a web
    site, database and a set of tools for the meta-analysis, re-use and sharing 
    of genomics data, currently primarily targeted at the analysis of gene 
    expression profiles. Gemma contains data from thousands of public studies, 
    referencing thousands of published papers. 

## Installation instructions


### Bioconductor
You can install `gemma.R` through [Bioconductor](http://bioconductor.org/) with the following code:

```{r 'install', eval = FALSE}
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gemma.R")
```


## Usage

To get started with `gemma.R`, read the [vignette](https://pavlidislab.github.io/gemma.R/articles/gemma.R.html).

## Citation

To cite Gemma, please use: [Lim, N. et al., Curation of over 10 000 transcriptomic studies to enable data reuse, Database, 2021.](https://doi.org/10.1093/database/baab006)

## Code of Conduct

Please note that `gemma.R` is released with the [Bioconductor Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.

Owner

  • Name: Pavlidis lab
  • Login: PavlidisLab
  • Kind: organization
  • Location: Vancouver, British Columbia, Canada

The Pavlidis Lab at the University of British Columbia

GitHub Events

Total
  • Issues event: 1
  • Delete event: 1
  • Push event: 125
  • Create event: 2
Last Year
  • Issues event: 1
  • Delete event: 1
  • Push event: 125
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 790
  • Total Committers: 11
  • Avg Commits per committer: 71.818
  • Development Distribution Score (DDS): 0.682
Past Year
  • Commits: 140
  • Committers: 5
  • Avg Commits per committer: 28.0
  • Development Distribution Score (DDS): 0.514
Top Committers
Name Email Commits
yavyx j****r@g****m 251
OganM o****i@g****m 242
OganM o****i@g****m 165
Jordan Sicherman j****n@m****a 92
jsicherman j****n 13
yavyx y****x 11
Paul Pavlidis p****l@m****a 8
Javier CastilloArnemann j****o@n****a 3
J Wokaty j****y 2
J Wokaty j****y@s****u 2
Guillaume Poirier-Morency g****y@g****m 1
Committer Domains (Top 20 + Academic)
msl.ubc.ca: 2 sph.cuny.edu: 1 nelson.msl.ubc.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 45
  • Total pull requests: 12
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 28 days
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.58
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • oganm (26)
  • jsicherman (9)
  • yavyx (6)
  • arteymix (4)
  • fratajcz (1)
Pull Request Authors
  • oganm (12)
  • yavyx (1)
  • arteymix (1)
Top Labels
Issue Labels
enhancement (10) bug (4) documentation (4) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 6,939 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 16
  • Total maintainers: 1
bioconductor.org: gemma.R

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

  • Versions: 16
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 6,939 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 31.2%
Downloads: 93.5%
Maintainers (1)
ogan.mancarci@gmail.com
Last synced: 6 months ago

Dependencies

.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
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  • bit64 * imports
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  • utils * imports
  • BiocStyle * suggests
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  • microbenchmark * suggests
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  • testthat >= 2.0.0 suggests
  • viridis * suggests