Statistical Inference via Data Science (A ModernDive into R and the Tidyverse)

by Chester Ismay and Albert Y. Kim

https://moderndive.com/index.html

Introduction to R, RStudio and the Tidyverse for visualizing, wrangling and analyzing your data.

Statistical Thinking for the 21st Century by Russell A. Poldrack

https://statsthinking21.github.io/statsthinking21-core-site/index.html#

Modern approach to introductory statistics, good sections on plotting and summarizing data.

Elements of Statistical Modeling for Experimental Biology by Jeffrey A. Walker

https://www.middleprofessor.com/files/applied-biostatistics_bookdown/_book/index.html

Takes a statistical modeling approach, focusing on estimates of effects and uncertainty.

R for Data Science by Garrett Grolemund & Hadley Wickham

https://r4ds.had.co.nz/index.html

Mostly covers details of using the tidyverse to import, wrangle and get your data ready to analyze. 

Introduction to Modern Statistics by Mine Çetinkaya-Rundel & Johanna Hardin

https://openintro-ims.netlify.app/index.html

Modern take on introductory statistics in an R based format.

Biological Statistics by John H. McDonald

https://stats.libretexts.org/Bookshelves/Applied_Statistics/Book%3A_Biological_Statistics_(McDonald)

More traditional statistics text, covering details of specific hypothesis tests (not R based, but useful background)

Modern Statistics for Modern Biology by Susan Holmes, Wolfgang Huber

https://www.huber.embl.de/msmb/introduction.html

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).

Analysis of community ecology data in R by David Zelený

https://www.davidzeleny.net/anadat-r/doku.php/en:start

Multivariate analysis including ordination (e.g., PCA, nMDS plots), cluster analysis and diversity analysis

Broadening Your Statistical Horizons: Generalized Linear Models and Multilevel Models By Julie Legler and Paul Roback

https://bookdown.org/roback/bookdown-bysh/ch-distthry.html

More advanced stats topics including Generalized Linear Models likelihood theory, zero-inflated Poisson, and parametric bootstrapping

R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire, Garrett Grolemund

https://bookdown.org/yihui/rmarkdown/

Everything you want to know about RMarkdown (no stats)