Extra resources
Developing R/Bioconductor packages for Genomics
Welcome
Program
Prerequesites
Extra resources
Day 1
Lecture 0 - Introduction to the workshop
Lecture 1 - R package architecture
Lecture 2 - Introduction to Bioconductor
Lecture 3 - R developer toolkit
Day 2
Lecture 4 - Continuous development
Lecture 5 - Bioconductor 201
Day 3
Lecture 6 - Git versioning
Lecture 8 - Vignettes and data
Day 4
Lecture 7 - S4 classes in Bioconductor
Lecture 9 - Bioconductor package submission
Day 5
Lecture 10 - Other package types
Lecture 11 - Package dissemination
Exercises
1
Getting started with Bioconductor ecosystem
2
Kickstarting an R package
3
Enriching package functionalities
4
Using S4 classes in a package
5
Improving package integration
Table of contents
R styling
R/Bioconductor programming
Scientific readings
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Extra resources
R styling
http://bioconductor.org/developers/how-to/coding-style/
https://jef.works/R-style-guide/
https://style.tidyverse.org/
https://google.github.io/styleguide/Rguide.html
R/Bioconductor programming
The
excellent R guide for beginners, by Emmanuel Paradis:
PDF
The more advanced
R for data science
book by Hadley Wickam himself:
https://r4ds.had.co.nz/
The
150+ pages comprehensive book to learn everything about Bioconductor. This ebook has been published by
Kasper D. Hansen
and is freely available under the
CC BY-NC-SA 4.0 license
:
PDF
Scientific readings
2014 Nat. Methods paper from Bioconductor core team describing important object classes
To see from how far Bioc comes from...
More research on osmotic stress reponse
Prerequesites
Lecture 0 - Introduction to the workshop