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methylGSA

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing

https://github.com/reese3928/methylgsa

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary

Keywords

enrichment generalized-linear-models logistic-regression methylation ontology shiny

Keywords from Contributors

differential-expression gene-expression transcriptomics genomics gene bioconductor-package sequencing rna-seq proteomics bioc
Last synced: 6 months ago · JSON representation

Repository

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing

Basic Info
Statistics
  • Stars: 13
  • Watchers: 1
  • Forks: 2
  • Open Issues: 4
  • Releases: 0
Topics
enrichment generalized-linear-models logistic-regression methylation ontology shiny
Created almost 8 years ago · Last pushed almost 5 years ago
Metadata Files
Readme

README.md

methylGSA

methylGSA is a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.

The Bioconductor package can be found here.
The Bioconductor package vignette can be found here.
The methylGSA paper can be found here.

Shiny app installation

The following packages are required to be installed before launching the app.
Packages from CRAN: {r} install.packages("DT") install.packages("ggplot2") install.packages("shinycssloaders")

Packages from Bioconductor:
If analyzing 450K array, IlluminaHumanMethylation450kanno.ilmn12.hg19 needs to be installed. {r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19") If analyzing EPIC array, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 needs to be installed. {r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")

Launch the app

After installation, the app can be launched with the following code: {r} library(methylGSA) methylGSA::runExample()

Step-by-step instructions

A step-by-step instructions on the workflow of the app can be found here.

Citation

Ren, X., & Kuan, P. F. (2019). methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics, 35(11), 1958-1959.

@article{ren2019methylgsa,
title={methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing},
author={Ren, Xu and Kuan, Pei Fen},
journal={Bioinformatics},
volume={35},
number={11},
pages={1958--1959},
year={2019},
publisher={Oxford University Press}
}

Owner

  • Name: Xu Ren
  • Login: reese3928
  • Kind: user

Staying at home.

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 55
  • Total Committers: 4
  • Avg Commits per committer: 13.75
  • Development Distribution Score (DDS): 0.473
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Xu Ren x****n@s****u 29
Xu Ren x****0@g****m 16
Nitesh Turaga n****a@g****m 8
vobencha v****a@g****m 2
Committer Domains (Top 20 + Academic)
stonybrook.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 7
  • Total pull request authors: 0
  • Average comments per issue: 1.14
  • 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
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Top Authors
Issue Authors
  • ellendejong (1)
  • jcabanad (1)
  • MSaadfarooq (1)
  • sam0per (1)
  • acarbome7 (1)
  • jakalssj3 (1)
  • BastiDucreux (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 17,226 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: methylGSA

Gene Set Analysis Using the Outcome of Differential Methylation

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 17,226 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 15.1%
Forks count: 15.3%
Average: 17.4%
Downloads: 56.4%
Maintainers (1)
xuren2120@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • AnnotationDbi * imports
  • BiocParallel * imports
  • GO.db * imports
  • IlluminaHumanMethylation450kanno.ilmn12.hg19 * imports
  • IlluminaHumanMethylationEPICanno.ilm10b4.hg19 * imports
  • RobustRankAggreg * imports
  • clusterProfiler * imports
  • ggplot2 * imports
  • missMethyl * imports
  • org.Hs.eg.db * imports
  • reactome.db * imports
  • shiny * imports
  • stats * imports
  • stringr * imports
  • enrichplot * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests