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prewas

R package to perform data pre-processing for more informative bacterial GWAS

https://github.com/snitkin-lab-umich/prewas

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
    6 of 11 committers (54.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary

Keywords

bacterial-genomes gwas gwas-tools microbiology r r-package
Last synced: 10 months ago · JSON representation

Repository

R package to perform data pre-processing for more informative bacterial GWAS

Basic Info
  • Host: GitHub
  • Owner: Snitkin-Lab-Umich
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 927 KB
Statistics
  • Stars: 5
  • Watchers: 3
  • Forks: 3
  • Open Issues: 8
  • Releases: 3
Topics
bacterial-genomes gwas gwas-tools microbiology r r-package
Created almost 7 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

prewas: data pre-processing for more informative bacterial GWAS

CRAN_Status_Badge

Introduction

The prewas R package allows users to create a binary SNP matrix from a whole genome alignment. The SNP matrix includes the following features: (1) multiple line representation of multiallelic sites, (2) multiple line representation for SNPs present in overlapping genes, and (3) choice over the reference allele. Additionally, users can collapse SNPs into genes so the output is a binary gene matrix. Output from the prewas package should be used as the input to bacterial GWAS tools such as hogwash.

Note: this package depends on R (>= 3.5.0).

For the most up-to-date package, it is recommended to install using dev.tools:

install.packages("devtools") devtools::install_github("Snitkin-Lab-Umich/prewas") library(prewas)

Documentation

prewas is described in the paper: "prewas: data pre-processing for more informative bacterial GWAS". The Rscripts and data for the paper's figures and analyses can be found in the manuscript analysis repository.

A tutorial explaining how to use the package can be found in the vignette.

Contributors

Katie Saund, Stephanie Thiede, and Zena Lapp contributed to this code.

Questions

Please open an issue or contact Evan Snitkin (esnitkin@umich.edu) with any questions.

Owner

  • Name: Snitkin-Lab-Umich
  • Login: Snitkin-Lab-Umich
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 312
  • Total Committers: 11
  • Avg Commits per committer: 28.364
  • Development Distribution Score (DDS): 0.449
Past Year
  • Commits: 9
  • Committers: 3
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.222
Top Committers
Name Email Commits
Katie Saund k****d@u****u 172
sthiede t****e@u****u 77
katiembrennan k****3@g****m 26
Zena Lapp z****p@u****u 13
Zena Lapp z****p@g****m 8
Ali Mohammed Pirani a****i@l****l 7
ecmaggioncalda 7****a 3
Stephanie Nicole Thiede t****e@f****u 2
Zena Lapp z****p@g****u 2
Snitkin-Lab-Umich 3****b 1
Zena Lapp z****p@g****u 1
Committer Domains (Top 20 + Academic)
umich.edu: 3 gl-login1.arc-ts.umich.edu: 1 gl-login2.arc-ts.umich.edu: 1 flux-login2.arc-ts.umich.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 14
  • Total pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 6 minutes
  • Total issue authors: 7
  • Total pull request authors: 1
  • Average comments per issue: 1.21
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • 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
  • zenalapp (5)
  • hsinjou0714 (3)
  • katiesaund (2)
  • HenrikBengtsson (1)
  • Albertzhuo123 (1)
  • sthiede (1)
  • Owuorgpo (1)
Pull Request Authors
  • alipirani88 (1)
Top Labels
Issue Labels
enhancement (1) bug (1) documentation (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: prewas

Data Pre-Processing for Bacterial Genome-Wide Association Studies

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 17.8%
Stargazers count: 24.2%
Average: 26.8%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
katiephd@umich.edu
Last synced: about 1 year ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • ape >= 5.3 imports
  • future >= 1.15.1 imports
  • future.apply >= 1.3.0 imports
  • methods >= 3.5.0 imports
  • phangorn >= 2.5.5 imports
  • stats >= 3.5.0 imports
  • utils >= 3.5.0 imports
  • vcfR >= 1.8.0 imports
  • knitr >= 1.24 suggests
  • rmarkdown >= 1.15 suggests
  • testthat >= 2.2.1 suggests