Online R & Stats Textbooks
(Includes R code unless otherwise noted)
Introduction to R, RStudio and the Tidyverse for visualizing, wrangling and analyzing your data.
Modern approach to introductory statistics, good sections on plotting and summarizing data.
Takes a statistical modeling approach, focusing on estimates of effects and uncertainty.
More traditional statistics text, covering details of specific hypothesis tests (not R based, but useful background)
Covers many modern approaches to data analysis, and many different types of data including RNA-Seq, flow-cytometry, taxa abundances, imaging data and single cell measurements. (Although some of the R code relies on Base R instead of Tidyverse functions).
Multivariate analysis including ordination (e.g., PCA, nMDS plots), cluster analysis and diversity analysis
More advanced stats topics including Generalized Linear Models likelihood theory, zero-inflated Poisson, and parametric bootstrapping