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‎.Rbuildignore‎

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^voomCLR\.Rproj$
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^\.Rproj\.user$
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^dev$
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^LICENSE\.md$
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^README\.Rmd$
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^codecov\.yml$
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^\.github$

‎.github/.gitignore‎

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*.html

‎.github/workflows/check-bioc.yml‎

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## Read more about GitHub actions the features of this GitHub Actions workflow
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## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
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##
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## For more details, check the biocthis developer notes vignette at
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## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
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##
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## You can add this workflow to other packages using:
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## > biocthis::use_bioc_github_action()
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##
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## Using GitHub Actions exposes you to many details about how R packages are
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## compiled and installed in several operating system.s
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### If you need help, please follow the steps listed at
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## https://github.com/r-lib/actions#where-to-find-help
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##
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## If you found an issue specific to biocthis's GHA workflow, please report it
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## with the information that will make it easier for others to help you.
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## Thank you!
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## Acronyms:
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## * GHA: GitHub Action
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## * OS: operating system
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on:
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push:
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pull_request:
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name: R-CMD-check-bioc
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## These environment variables control whether to run GHA code later on that is
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## specific to testthat, covr, and pkgdown.
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##
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## If you need to clear the cache of packages, update the number inside
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## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
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## Note that you can always run a GHA test without the cache by using the word
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## "/nocache" in the commit message.
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env:
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has_testthat: 'false'
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run_covr: 'false'
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run_pkgdown: 'false'
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has_RUnit: 'false'
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cache-version: 'cache-v1'
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run_docker: 'false'
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jobs:
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build-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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container: ${{ matrix.config.cont }}
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## Environment variables unique to this job.
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strategy:
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fail-fast: false
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matrix:
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config:
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- { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
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- { os: macOS-latest, r: '4.2', bioc: '3.15'}
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- { os: windows-latest, r: '4.2', bioc: '3.15'}
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## Check https://github.com/r-lib/actions/tree/master/examples
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## for examples using the http-user-agent
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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NOT_CRAN: true
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TZ: UTC
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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## Set the R library to the directory matching the
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## R packages cache step further below when running on Docker (Linux).
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- name: Set R Library home on Linux
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if: runner.os == 'Linux'
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run: |
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mkdir /__w/_temp/Library
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echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
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## Most of these steps are the same as the ones in
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## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
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## If they update their steps, we will also need to update ours.
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- name: Checkout Repository
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uses: actions/checkout@v2
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## R is already included in the Bioconductor docker images
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- name: Setup R from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-r@v2-branch
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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## pandoc is already included in the Bioconductor docker images
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- name: Setup pandoc from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-pandoc@v2-branch
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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- name: Restore R package cache
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
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- name: Cache R packages on Linux
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
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uses: actions/cache@v2
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with:
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path: /home/runner/work/_temp/Library
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
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- name: Install Linux system dependencies
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if: runner.os == 'Linux'
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run: |
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sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
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echo $sysreqs
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sudo -s eval "$sysreqs"
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- name: Install macOS system dependencies
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if: matrix.config.os == 'macOS-latest'
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run: |
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## Enable installing XML from source if needed
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brew install libxml2
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echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
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## Required to install magick as noted at
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## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
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brew install imagemagick@6
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## For textshaping, required by ragg, and required by pkgdown
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brew install harfbuzz fribidi
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## For installing usethis's dependency gert
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brew install libgit2
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## Required for tcltk
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brew install xquartz --cask
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- name: Install Windows system dependencies
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if: runner.os == 'Windows'
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run: |
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## Edit below if you have any Windows system dependencies
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shell: Rscript {0}
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- name: Install BiocManager
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run: |
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message(paste('****', Sys.time(), 'installing BiocManager ****'))
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remotes::install_cran("BiocManager")
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shell: Rscript {0}
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- name: Set BiocVersion
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run: |
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BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
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shell: Rscript {0}
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- name: Install dependencies pass 1
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run: |
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## Try installing the package dependencies in steps. First the local
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## dependencies, then any remaining dependencies to avoid the
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## issues described at
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## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
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## https://github.com/r-lib/remotes/issues/296
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## Ideally, all dependencies should get installed in the first pass.
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## Set the repos source depending on the OS
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## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
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## though based on https://bit.ly/bioc2021-package-binaries
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## the Azure link will be the main one going forward.
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gha_repos <- if(
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.Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
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) c(
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"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.15/bioc",
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BiocManager::repositories()
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) else BiocManager::repositories()
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## For running the checks
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message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
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install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
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## Pass #1 at installing dependencies
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## This pass uses AnVIL-powered fast binaries
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## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
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## The speed gains only apply to the docker builds.
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message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
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remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
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continue-on-error: true
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shell: Rscript {0}
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- name: Install dependencies pass 2
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run: |
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## Pass #2 at installing dependencies
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## This pass does not use AnVIL and will thus update any packages
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## that have seen been updated in Bioconductor
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message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
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remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
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shell: Rscript {0}
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- name: Install BiocGenerics
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if: env.has_RUnit == 'true'
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run: |
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## Install BiocGenerics
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BiocManager::install("BiocGenerics")
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shell: Rscript {0}
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- name: Install covr
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if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
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remotes::install_cran("covr")
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shell: Rscript {0}
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- name: Install pkgdown
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if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
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remotes::install_cran("pkgdown")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- installed.packages()[, "Package"]
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Run CMD check
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env:
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_R_CHECK_CRAN_INCOMING_: false
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DISPLAY: 99.0
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(
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args = c("--no-manual", "--no-vignettes", "--timings"),
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build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
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error_on = "error",
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check_dir = "check"
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)
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shell: Rscript {0}
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## Might need an to add this to the if: && runner.os == 'Linux'
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- name: Reveal testthat details
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if: env.has_testthat == 'true'
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run: find . -name testthat.Rout -exec cat '{}' ';'
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- name: Run RUnit tests
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if: env.has_RUnit == 'true'
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run: |
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BiocGenerics:::testPackage()
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shell: Rscript {0}
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- name: Run BiocCheck
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env:
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DISPLAY: 99.0
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run: |
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BiocCheck::BiocCheck(
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dir('check', 'tar.gz$', full.names = TRUE),
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`quit-with-status` = TRUE,
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`no-check-R-ver` = TRUE,
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`no-check-bioc-help` = TRUE
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)
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shell: Rscript {0}
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- name: Test coverage
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if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
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covr::codecov()
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shell: Rscript {0}
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- name: Install package
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if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: R CMD INSTALL .
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- name: Build and deploy pkgdown site
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if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "[email protected]"
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Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
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shell: bash {0}
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## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
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## at least one locally before this will work. This creates the gh-pages
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## branch (erasing anything you haven't version controlled!) and
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## makes the git history recognizable by pkgdown.
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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with:
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name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
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path: check
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## Note that DOCKER_PASSWORD is really a token for your dockerhub
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## account, not your actual dockerhub account password.
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## This comes from
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## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
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## Check https://github.com/docker/build-push-action/tree/releases/v1
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## for more details.
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- uses: docker/build-push-action@v1
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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repository: koenvandenberge/voomclr
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tag_with_ref: true
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tag_with_sha: true
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tags: latest

‎.gitignore‎

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lint_results.txt
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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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*.Rproj
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.Rdata
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.httr-oauth
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.DS_Store
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inst/doc

‎DESCRIPTION‎

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Package: voomCLR
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Title: Compositional analysis of cell count data.
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Version: 0.99.37
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Authors@R:
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person("Koen", "Van den Berge", , "[email protected]", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-1833-8478"))
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Description: voomCLR allows for compositional analysis of cell (type/state) counts, taking
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into account heteroscedasticity and bias. It transforms cell count data using the
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centered-log-ratio (CLR) transformation, and estimates observation-level variances
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by leveraging the limma-voom framework and codebase or calculating them analytically.
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Residual variances are shrunken using the limma empirical Bayes technique.
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Finally, a bias correction is applied as recommended in Zhou et al. (2022),
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10.1186/s13059-022-02655-5. The uncertainty involved in estimating the bias term can be
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taken into account using bootstrapping.
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biocViews: software, single-cell.
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License: GPL (>= 3)
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.2.3
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Imports:
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limma,
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methods,
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statmod,
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modeest,
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mixtools,
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edgeR
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Suggests:
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BiocStyle,
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covr,
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knitr,
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RefManageR,
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rmarkdown,
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sessioninfo,
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testthat (>= 3.0.0)
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Config/testthat/edition: 3
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VignetteBuilder: knitr
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Collate:
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'utils.R'
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'applyBiasCorrection.R'
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'plotBeta.R'
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'topTableBC.R'
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'voomALR.R'
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'voomCLR.R'

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