README.md

Interesting Online Books

Online books regarding:

Open Science

• The Open Science Training Handbook
  https://open-science-training-handbook.github.io/Open-Science-Training-Handbook_EN/

R best practises

• R for Data Science
  https://r4ds.had.co.nz/
  by
  Garrett Grolemund, Hadley Wickham

• R for Data Science: Exercise Solutions
  https://jrnold.github.io/r4ds-exercise-solutions/
  by
  Jeffrey B. Arnold

• Advanced R
  https://adv-r.hadley.nz/
  by
  Hadley Wickham

• Advanced R Solutions
  https://advanced-r-solutions.rbind.io/
  by
  Malte Grosser, Henning Bumann & Hadley Wickham

• What They Forgot to Teach You About R
  https://rstats.wtf/index.html
  by
  Jennifer Bryan & Jim Hester

• Modern R with the tidyverse
  https://modern-rstats.eu/
  by
  Bruno Rodrigues

• Tidyverse Cookbook
  https://bookdown.org/Tazinho/Tidyverse-Cookbook/
  by
  Malte Grosser

• R Markdown: The Definitive Guide
  https://bookdown.org/yihui/rmarkdown/
  by
  Yihui Xie, J. J. Allaire, Garrett Grolemund

• The tidyverse style guide
  https://style.tidyverse.org/
  by
  Hadley Wickham

• R Style Guide Best practices for readable, sharable, and verifiable R code
  https://jef.works/R-style-guide/
  by
  Jean Fan

• R packages
  https://r-pkgs.org/
  by
  Hadley Wickham

• Data Wrangling
  https://dcl-wrangle.stanford.edu/index.html
  by
  Sara Altman, Bill Behrman

• Fundamentals of Data Visualization
  https://clauswilke.com/dataviz/index.html
  by
  Claus O. Wilke

• ComplexHeatmap Complete Reference
  https://jokergoo.github.io/ComplexHeatmap-reference/book/
  by
  Zuguang Gu

• Statistical Inference via Data Science: A ModernDive into R and the Tidyverse
  https://moderndive.com/index.html by
  Chester Ismay, Albert Y. Kim

Machine Learning with R

• An Introduction to Machine Learning with R
  https://lgatto.github.io/IntroMachineLearningWithR/index.html
  by
  Laurent Gatto

• TPOT and the Automatic Statistician
  http://thllwg.de/tpotr/
  by
  Thorben Hellweg, Christopher Olbrich, Christian Werner

Single cell RNA analysis

• Orchestrating Single-Cell Analysis with Bioconductor
  https://osca.bioconductor.org/
  by
  Robert Amezquita

• Aaron’s single-cell thoughts
  https://ltla.github.io/SingleCellThoughts/
  by
  Aaron Lun

• Analysis of single cell RNA-seq data
  https://scrnaseq-course.cog.sanger.ac.uk/website/index.html
  by
  Vladimir Kiselev

Bioconductor

• The Bioconductor 2018 Workshop Compilation
  https://bioconductor.github.io/BiocWorkshops/
  editors
  Levi Waldron Sean Davis Marce Ramos Lori Shepherd Martin Morgan

• Operations on Genomic Intervals with GenomicRanges package
  https://al2na.github.io/compgenr/genomic_intervals/granges.html
  by
  Altuna Akalin

• Computational Genomics with R
  https://compgenomr.github.io/book/
  by
  Altuna Akalin

Statistics

• Modern Statistics for Modern Biology
  https://web.stanford.edu/class/bios221/book/
  by
  Susan Holmes, Wolfgang Huber

Git / GitHub

• Happy Git and GitHub for the useR
  https://happygitwithr.com/
  by
  Jenny Bryan, the STAT 545 TAs, Jim Hester

Github pages

• Creating websites in R
  https://www.emilyzabor.com/tutorials/rmarkdown_websites_tutorial.html
  by
  Emily C. Zabor

• Blogdown: Creating Websites with R Markdown
  https://bookdown.org/yihui/blogdown/
  by
  Yihui Xie, Amber Thomas, Alison Presmanes Hill

PH525x series - Biomedical Data Science

http://genomicsclass.github.io/book/

Biomedical Knowledge Mining using GOSemSim and clusterProfiler

https://yulab-smu.top/biomedical-knowledge-mining-book/index.html
by
Guangchuang Yu

Shiny

• Building Shiny apps - an interactive tutorial
  https://deanattali.com/blog/building-shiny-apps-tutorial/#1-before-we-begin
  by
  Dean Attali

• Mastering Shiny
  https://mastering-shiny.org/
  by
  Hadley Wickham

• Engineering Production-Grade Shiny Apps
  https://engineering-shiny.org/index.html
  by
  Colin Fay, Sébastien Rochette, Vincent Guyader and Cervan Girard