├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug-report.md │ ├── config.yml │ └── feature-request.md ├── pull_request_template.md └── workflows │ └── check-package.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── curatedMetagenomicData-defunct.R ├── curatedMetagenomicData.R ├── mergeData.R ├── returnSamples.R ├── sampleMetadata.R ├── sysdata.rda └── where.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── curatedMetagenomicData.Rproj ├── data-raw ├── phylogeneticTree.R ├── resourceTitles.R ├── rowData.R ├── sampleMetadata.R └── sysdata.R ├── data └── sampleMetadata.rda ├── inst ├── CITATION ├── extdata │ ├── 2021-03-31.csv │ ├── 2021-04-02.csv │ ├── 2021-10-14.csv │ ├── 2022-04-13.csv │ ├── 2022-10-19.csv │ └── metadata.csv └── scripts │ ├── make-data.R │ └── make-metadata.R ├── man ├── curatedMetagenomicData-defunct.Rd ├── curatedMetagenomicData.Rd ├── mergeData.Rd ├── returnSamples.Rd └── sampleMetadata.Rd ├── tests ├── testthat.R └── testthat │ ├── test-curatedMetagenomicData.R │ ├── test-mergeData.R │ ├── test-returnSamples.R │ └── test-sampleMetadata.R └── vignettes ├── .gitignore ├── articles ├── available-studies.Rmd ├── our-pipeline.Rmd └── version-three.Rmd └── curatedMetagenomicData.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/waldronlab/curatedMetagenomicData/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug-report.md: -------------------------------------------------------------------------------- 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