Biostats
Biostatistical Design and Analysis Using R: A Practical Guide book. A free book on how to use R.
Exploratory Data Analysis with R by Dr. Peng free book
Regression and other stories book
Data science and predictive analytics shortcuts and tips at UMich
Program tutorials
Need help remembering all those lines in R? Check out these cheat sheets.
Sequence Data Analysis Programs
Mothur is “a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.”
“QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.”
RSTudio is a Graphical User Interface (GUI) that will make learning and using R significantly easier for some folks.
Data Visualization
The Seeing Theory website has some great tools for visualizing statistics, including interactive graphs, equations for determining various measurements, and explanations of concepts in statistics.
Fundamentals of Data Visualization is a free on-line book preview by Claus Wilke that provides how-to guides for creating graphs and infographics that best describe your data. Interesting side note: The book was written entirely in R Markdown, and the source code is on GitHub.