Initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.github/.gitignore

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+*.html

.github/workflows/build-book-release.yml

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+## Read more about GitHub actions the features of this GitHub Actions workflow
+## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
+##
+## For more details, check the biocthis developer notes vignette at
+## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
+##
+## You can add this workflow to other packages using:
+## > biocthis::use_bioc_github_action()
+##
+## Using GitHub Actions exposes you to many details about how R packages are
+## compiled and installed in several operating system.s
+### If you need help, please follow the steps listed at
+## https://github.com/r-lib/actions#where-to-find-help
+##
+## If you found an issue specific to biocthis's GHA workflow, please report it
+## with the information that will make it easier for others to help you.
+## Thank you!
+
+## Acronyms:
+## * GHA: GitHub Action
+## * OS: operating system
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: build-book-release
+
+## These environment variables control whether to run GHA code later on that is
+## specific to testthat, covr, and pkgdown.
+##
+## If you need to clear the cache of packages, update the number inside
+## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
+## Note that you can always run a GHA test without the cache by using the word
+## "/nocache" in the commit message.
+env:
+  has_testthat: 'false'
+  run_covr: 'false'
+  run_pkgdown: 'false'
+  has_RUnit: 'false'
+  cache-version: 'cache-v1'
+
+jobs:
+  build-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    ## Environment variables unique to this job.
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      NOT_CRAN: true
+      TZ: UTC
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+
+      ## Set the R library to the directory matching the
+      ## R packages cache step further below when running on Docker (Linux).
+      - name: Set R Library home on Linux
+        if: runner.os == 'Linux'
+        run: |
+          mkdir /__w/_temp/Library
+          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
+
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
+
+      - name: Install BiocManager
+        run: |
+          message(paste('****', Sys.time(), 'installing BiocManager ****'))
+          remotes::install_cran("BiocManager")
+        shell: Rscript {0}
+
+      - name: Set BiocVersion
+        run: |
+          BiocManager::install(version = "devel", ask = FALSE)
+        shell: Rscript {0}
+
+      - name: Cache R packages on Linux
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
+        uses: actions/cache@v1
+        with:
+          path: /home/runner/work/_temp/Library
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+          sudo apt-get install -y libcurl4-openssl-dev libglpk-dev
+
+      - name: Install bookdown
+        if: github.ref == 'refs/heads/main' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("bookdown")
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          ## Try installing the package dependencies in steps. First the local
+          ## dependencies, then any remaining dependencies to avoid the
+          ## issues described at
+          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
+          ## https://github.com/r-lib/remotes/issues/296
+          ## Ideally, all dependencies should get installed in the first pass.
+
+          BiocManager::install("HDF5Array")
+          BiocManager::install("fionarhuang/TreeSummarizedExperiment")
+          library("dplyr")	  
+
+          ## Pass #1 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force=TRUE)
+
+          ## Pass #2 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force=TRUE)
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          remotes::install_cran("rcmdcheck")
+          BiocManager::install("BiocCheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Bookdown Deploy Preparation
+        if: github.ref == 'refs/heads/main' && runner.os == 'Linux'
+        run: |
+          git fetch --all
+          commit=$(git --work-tree=../ rev-parse --verify --short HEAD)
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git worktree add --track -B gh-pages docs origin/gh-pages
+
+      - name: Bookdown
+        if: runner.os == 'Linux'
+        run: |
+          Rscript -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")'
+      
+      - name: Bookdown pdf
+        if: runner.os == 'Linux'
+        run: |
+          Rscript -e 'tinytex::install_tinytex()'
+          Rscript -e 'bookdown::render_book("index.Rmd", "bookdown::pdf_book")'
+
+      - name: Bookdown Deploy
+        if: github.ref == 'refs/heads/main' && runner.os == 'Linux'
+        run: |
+          cd docs
+          git add -A .
+          git commit --allow-empty -m "Build book @$(git rev-parse --short HEAD)"
+          git push --force origin HEAD:gh-pages
+          cd ..
+
+      - name: Upload check results
+        if: runner.os == 'Linux' && failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-biocversion-devel-r-4.1-results
+          path: docs

.gitignore

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+07-beta_files/
+_bookdown_files
+notes
+*~
+# History files
+.Rhistory
+.Rapp.history
+# Session Data files
+.RData
+# User-specific files
+.Ruserdata
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+# R Environment Variables
+.Renviron
+course_2021_radboud.Rproj

01-program.Rmd

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+
+# Program
+
+The course takes place on each working day from 9am – 1pm
+(CEST). Short breaks will be scheduled between sessions.
+
+The hands-on sessions consist of a set of questions and example
+data. Solve the exercises by taking advantage of the online examples
+and resources that are pointed out in the study material. There is
+often more than one way to solve a given task. It is assumed that you
+have already installed the required software. Do not hesitate to ask
+support from the course assistants.
+
+## Day 1: from raw sequences to ecological data analysis
+
+**Lectures**
+
+ * Microbiota analysis: association studies vs. causality; microbiota sequencing methods (16S, shotgun, metagenomics) - by dr. Tom Ederveen (Radboud UMC Nijmegen, The Netherlands)
+
+ * DNA isolation and 16S rRNA gene sequencing; bioinformatics step 1: from raw sequences to OTU table in a biom file – by Tom Ederveen (Radboudumc Nijmegen, The Netherlands)
+
+
+**Demo & Practical**
+
+ * Importing data to R for interactive data analysis 
+
+ * Task: initialize reproducible report
+
+----------------------------------------------------------------
+
+## Day 2 - Alpha diversity 
+
+**Demo**
+
+- Microbiome data exploration
+
+**Lecture**
+
+- Key concepts in microbiome data science
+
+**Practical**
+
+- Alpha diversity: estimation, analysis, and visualization 
+
+----------------------------------------------------------------
+
+## Day 3 - Beta diversity
+
+**Demo**
+
+- Community similarity 
+
+**Practical**
+
+- Beta diversity: estimation, analysis, and visualization
+
+-----------------------------------------------------------------
+
+## Day 4- Differential abundance
+
+**Lecture**
+
+- Differential abundance analysis methods 
+
+
+**Practical**
+
+- Differential abundance in practice
+
+
+**Lecture**
+
+- Overview of microbiota data science methods & concepts
+
+-----------------------------------------------------------------
+
+## Day 5 : Presentations & closing
+
+**Student presentations** on microbiome data analytics
+
+
+
+