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cogena

co-expressed gene-set enrichment analysis

https://github.com/zhilongjia/cogena

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.5%) to scientific vocabulary

Keywords

bioconductor bioinformatics package r

Keywords from Contributors

bioconductor-package genomics gene proteomics transcriptomics proteomics-data chip-seq mass-spectrometry looking-for-maintainer spatial-proteomics
Last synced: 6 months ago · JSON representation

Repository

co-expressed gene-set enrichment analysis

Basic Info
Statistics
  • Stars: 12
  • Watchers: 1
  • Forks: 7
  • Open Issues: 0
  • Releases: 0
Topics
bioconductor bioinformatics package r
Created about 11 years ago · Last pushed over 2 years ago
Metadata Files
Readme

README.Rmd 

---
title: "README"
author: "Zhilong Jia"
date: '2022-07-29'
output:
  md_document:
    variant: gfm
html_preview: false
---
# cogena

```{r setup, include=FALSE}
library("badger")
```

```{r, echo = FALSE, results='asis'}
cat(
    badge_bioc_release("cogena", "green"),
	badge_bioc_download("cogena", "total", "blue", "total"),
	badge_github_actions()
)
```


 [![releaseVersion](http://img.shields.io/badge/release%20version-1.14.0-green.svg?style=flat)](http://bioconductor.org/packages/cogena) [![develVersion](http://img.shields.io/badge/devel%20version-1.15.0-green.svg?style=flat)](http://github.com/zhilnogjia/cogena) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/cogena.svg)](https://www.bioconductor.org/packages/devel/bioc/html/cogena.html#since) [![Build](http://bioconductor.org/shields/build/devel/bioc/cogena.svg)](http://www.bioconductor.org/packages/devel/bioc/html/cogena.html)
[![download_Fromconda](https://anaconda.org/bioconda/bioconductor-cogena/badges/downloads.svg)](https://anaconda.org/bioconda/bioconductor-cogena/badges)
[![download_FromBioc](https://img.shields.io/badge/download-14692/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/cogena)

## Introduction
To discovery smaller scale, but highly correlated cellular events that may be of great biological relevance, co-expressed gene set enrichment analysis, cogena, aims to cluster gene expression profiles (coExp) for gene co-expression analysis and then implement enrichment analysis for each clusters (clEnrich) based on hyper-geometric test. The results can be visulised by heatmapCluster and heatmapPEI. Based on different gene sets used, cogena can be used as a tool for pathway analysis, GO enrichment analysis, drug repositioning and so on. See [vignette](http://bioconductor.org/packages/devel/bioc/vignettes/cogena/inst/doc/cogena-vignette_html.html) for the detailed workflow. 

The version of cogena at github is also availiable at [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/cogena.html) (development version)


## The workflow of cogena
![cogena_workflow](inst/figure/Cogena_workflow.png)

## Installation
devtools::install_github("zhilongjia/cogena")

## Help
[cogena in Biostars](https://www.biostars.org/p/137330/)


## Citation
[Jia, Zhilong, et al. "Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery." BMC Genomics 17.1 (2016): 1.](http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2737-8)


## Acknowledgement
cogena was originally based on the [clValid](http://cran.r-project.org/web/packages/clValid/index.html) package.

Owner

  • Name: Zhilong
  • Login: zhilongjia
  • Kind: user

A bioinformatician.

GitHub Events

Total
  • Fork event: 1
Last Year
  • Fork event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 416
  • Total Committers: 12
  • Avg Commits per committer: 34.667
  • Development Distribution Score (DDS): 0.214
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zhilong Jia z****a@g****m 327
z.jia z****a@b****8 59
Dan Tenenbaum d****a@f****g 8
Herve Pages h****s@f****g 4
Nitesh Turaga n****a@g****m 4
d.tenenbaum d****m@b****8 4
Hervé Pagès h****s@f****g 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Zhilong z****a 2
Sonali Arora s****a@f****g 1
s.arora s****a@b****8 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 roswellpark.org: 1 fredhutch.org: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 9
  • Total pull requests: 1
  • Average time to close issues: 5 months
  • Average time to close pull requests: 16 minutes
  • Total issue authors: 8
  • Total pull request authors: 1
  • Average comments per issue: 1.67
  • Average comments per pull request: 0.0
  • 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
View more stats
Top Authors
Issue Authors
  • IyadSultan (2)
  • BastienGamboa (1)
  • heylookabed (1)
  • puneetvaza (1)
  • limingxiang (1)
  • nandhinik2 (1)
  • llrs (1)
  • steph-e (1)
Pull Request Authors
  • zhilongjia (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 23,359 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: cogena

co-expressed gene-set enrichment analysis

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 23,359 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 15.1%
Downloads: 45.2%
Maintainers (1)
zhilongjia@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • cluster * depends
  • ggplot2 * depends
  • kohonen * depends
  • Biobase * imports
  • amap * imports
  • apcluster * imports
  • biwt * imports
  • class * imports
  • corrplot * imports
  • devtools * imports
  • doParallel * imports
  • dplyr * imports
  • fastcluster * imports
  • foreach * imports
  • gplots * imports
  • mclust * imports
  • methods * imports
  • parallel * imports
  • reshape2 * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • knitr * suggests
  • rmarkdown >= 2.1 suggests
.github/workflows/r.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite