Workshops for learning Bioconductor
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README.md

knit title description site github-repo documentclass
bookdown::render_book
The Bioconductor 2018 Workshop Compilation
This book is a central repository for all the workshops submitted to the Bioconductor 2018 Conference
bookdown::bookdown_site
Bioconductor/BiocWorkshops
book

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

The most up-to-date error messages and .md files from builds of individual workshops are here.

Introduction

Author: Martin Morgan^[Roswell Park Comprehensive Cancer Center, Buffalo, NY].
Last modified: 22 May, 2018.

The most recently compiled version of the book is available at https://bioconductor.github.io/BiocWorkshops/.

For Everyone

This book contains workshops used in R / Bioconductor training. The workshops are divided into 3 sections:

  • Learn (100-series chapters) contains material for beginning users of R and Bioconductor. The Bioconductor-related material is relevant even for experienced R users who are new to Bioconductor.

  • Use (200-series chapters) contains workshops emphasizing use of Bioconductor for common tasks, e.g., bulk RNA-seq differential expression, ChIP-seq, single-cell analysis, gene set enrichment, and annotation.

  • Develop (500-series chapters) contains workshops to help expert users hone their skills and contribute their domain-specific knowledge to the Bioconductor community.

For Workshop Authors

To contribute a new workshop, open a BiocWorkshops issue asking to be added as a collaborator.

DESCRIPTION

Update the DESCRIPTION file adding packages utilized in your workshop to the Imports field. Please be kind and don't remove anyone elses packages from the DESCRIPTION as this is a shared file for all workshops. Also don't add your packages to the Depends field.

Classifying your workshop

Follow the numbering scheme above to classify your workshop by preceding your title with "Bioconductor 1xx:", "Bioconductor 2xx:", or "Bioconductor 5xx:". Final workshop numbers will be determined by an editor.

Bookdown

Write your workshop as a stand-alone markdown document, using your workshop syllabus already posted here as a starting point. We are using bookdown ('knit-then-merge' strategy) to compile the workshops and produce a book that will be available through Continuous Integration at https://bioconductor.github.io/BiocWorkshops/.

You do not need to build the complete book yourself, it is sufficient to ensure that your own workshop compiles successfully. You can 1) compile draft versions using a standard "knit" procedure to compile your chapter, and 2) follow these bookdown procedures to see how your chapter will look in the finished product. Install the bookdown package package from CRAN, as well as pandoc. Render your chapter with the preview= option to render_book(), e.g.,

Rscript -e "bookdown::render_book(                             \
    'xxx_Your_Workshop.Rmd', 'bookdown::gitbook', preview=TRUE \
)"

As this is a shared space for all workshop contributors, in order to use the above command in the BiocWorkshops directory, the index has to be built at least once, which can be time consuming depending on how many workshops have already been submitted.

Rscript -e "bookdown::render_book(                             \
    'index.Rmd', 'bookdown::gitbook')"

To avoid having to build all workshops but still be able to preview your individual workshop we recommend creating a soft link to your .Rmd file. We recommend having the file in the BiocWorkshop/ and the soft link in any other directory on your system. By default, this will generate an html file in _book/ wherever this command is run.

mkdir tmp
cd tmp/
ln -s ../xxx_Your_Workshop.Rmd
Rscript -e "bookdown::render_book(                             \
    'xxx_Your_Workshop.Rmd', 'bookdown::gitbook', preview=TRUE \
)"

Push only your .Rmd file to the BiocWorkshop repository; the book will be rebuilt manually or automatically. Eventually the output will be available for end-users at https://bioconductor.github.io/BiocWorkshops .The master branch will not contain the built version of the book. Switching to the gh-pages branch will show built output.

Deadlines for Bioc2018

Please be aware of the following deadlines for the Bioconductor 2018 Conference in Toronto

  • Fri June 29: draft workshop materials submitted to this Bioconductor GitHub bookdown site

  • Fri July 6: feedback period completes

  • Weds July 18: workshops must pass checks without errors or warnings (All materials will be checked by Continuous Integration)

  • Thurs / Fri July 26-27: Bioc2018