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madpop

MHC Allele-Based Differencing between Populations

https://github.com/mlysy/madpop

Science Score: 26.0%

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Scientific vocabulary similarity
    Low similarity (8.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

MHC Allele-Based Differencing between Populations

Basic Info
  • Host: GitHub
  • Owner: mlysy
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 1.02 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created over 9 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License

README.md

MADPop: MHC Allele-Based Differencing Between Populations

Martin Lysy, Peter W.J. Kim, Terin Robinson

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Description

Tools for the analysis of population differences using the Major Histocompatibility Complex (MHC) genotypes of samples having a variable number of alleles (1-4) recorded for each individual. A hierarchical Dirichlet-Multinomial model on the genotype counts is used to pool small samples from multiple populations for pairwise tests of equality. Bayesian inference is implemented via the rstan package. Bootstrapped and posterior p-values are provided for chi-squared and likelihood ratio tests of equal genotype probabilities.

Installation

To install the latest R release: r install.packages("MADPop")

To install the latest development version, first install the R package devtools then run r devtools::install_github("mlysy/MADPop")

Usage

Please see tutorial here or by running vignette("MADPop-quicktut").

Owner

  • Login: mlysy
  • Kind: user
  • Company: University of Waterloo

Martin Lysy

GitHub Events

Total
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 62
  • Total Committers: 2
  • Avg Commits per committer: 31.0
  • Development Distribution Score (DDS): 0.065
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
mlysy m****y 58
Andrew Johnson a****n@a****m 4
Committer Domains (Top 20 + Academic)
arjohnsonau.com: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 months
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 2.25
  • Merged pull requests: 2
  • 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
Pull Request Authors
  • andrjohns (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 231 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: MADPop

MHC Allele-Based Differencing Between Populations

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 231 Last month
Rankings
Forks count: 21.9%
Dependent packages count: 29.8%
Stargazers count: 31.7%
Average: 33.1%
Dependent repos count: 35.5%
Downloads: 46.6%
Maintainers (1)
mlysy@uwaterloo.ca
Last synced: 11 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 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
  • R >= 3.4.0 depends
  • rstan >= 2.26.0 depends
  • Rcpp >= 0.12.0 imports
  • methods * imports
  • rstantools * imports
  • stats * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests