7 biocthis introduction

Instructor: Leo

7.1 Related past materials

I’ve taught a lot about biocthis over the years. Here’s a 2020 video:

and more recently, these are the LIBD rstats club 2023-03-10 notes. ¹

7.2 biocthis main commands

• https://bioconductor.org/packages/biocthis
• pkgdown documentation website: https://lcolladotor.github.io/biocthis/
  • biocthis::use_bioc_pkg_templates() documentation: https://lcolladotor.github.io/biocthis/reference/use_bioc_pkg_templates.html

These are the main steps you will need to know to make a Bioconductor package with biocthis:

1. You first will need to create a package using a command from usethis.

• For example: usethis::create_package("~/Desktop/cshl2023pkg")

2. Now that you have a package, we can use biocthis to create 4 template R scripts that will guide you and help you make the full structure for a Bioconductor R package.

• On your new R package (cshl2023pkg), we can now use biocthis::use_bioc_pkg_templates().

In part these commands were born out of my own self interest to make it easier to make new packages instead of copy-pasting the contents of an older one, then manually adjusting all the pieces for a new package. See https://lcolladotor.github.io/pkgs/ for the list of all the R packages I’ve been involved in.

7.3 Live demo

Here is the live demo result https://github.com/lcolladotor/cshl2023pkg/ with its companion documentation website at https://lcolladotor.github.io/cshl2023pkg/. Note that you will currently need the development version of biocthis which addresses the issues documented at https://github.com/r-lib/usethis/issues/1856.

## Install biocthis development version
BiocManager::install("lcolladotor/biocthis")

Check the git commit history at https://github.com/lcolladotor/cshl2023pkg/commits/devel and the GitHub Actions history at https://github.com/lcolladotor/cshl2023pkg/actions. We can see at https://app.codecov.io/gh/lcolladotor/cshl2023pkg the code coverage results for this demonstration package.

7.4 Community

For more materials on R/Bioconductor package development check http://contributions.bioconductor.org/.

I’m on a Friday night mood now enjoying @lmwebr’s #OSTA workshop 🔥, feeling grateful 🙏🏽 to everyone who nominated me for the #BioC2021 community award 🥇& celebrating 🍺 https://t.co/2oFLdGO3Uh

See you in #BioC2022🤞🏽 @Bioconductor #rstats @CDSBMexico https://t.co/0SGHDfiRCs pic.twitter.com/UmM9nMP2W2

— 🇲🇽 Leonardo Collado-Torres (@lcolladotor) August 7, 2021

biocthis is one of the reasons for my 2021 Bioconductor community award :-)

Do you want to play an active role? Join the cloud-working-group Slack channel.

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1. Soon I’ll process and upload the video to YouTube. By soon, I mean, later this summer.↩︎

© 2011-2023. All thoughts and opinions here are my own. The icon was designed by Mauricio Guzmán and is inspired by Huichol culture; it represents my community building interests.

This work is licensed under CC BY NC SA 4.0

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