14 Life Sciences

14.1 Assigning cell types with SingleR

[Aaron Lun]((<https://osca.bioconductor.org/contributors.html>)

This book covers the use of SingleR, one implementation of an automated annotation method for cell type annotation.

<https://bioconductor.org/books/3.12/SingleRBook/>

14.2 Computational Genomics with R

Altuna Akalin

The aim of this book is to provide the fundamentals for data analysis for genomics. We developed this book based on the computational genomics courses we are giving every year.

<http://compgenomr.github.io/book/>

14.3 Data Analysis for the Life Sciences

Rafael A Irizarry and Michael I Love

Data analysis is now part of practically every research project in the life sciences. In this book we use data and computer code to teach the necessary statistical concepts and programming skills to become a data analyst. Instead of showing theory first and then applying it to toy examples, we start with actual applications.

Pay what you want for the ebook, minimum $0.00

https://leanpub.com/dataanalysisforthelifesciences

Accompanying website

14.4 Git and Github for Advanced Ecological Data Analysis

Alexa Fredston

This material was prepared for a three-hour virtual session to teach Git and Github to a graduate-level course on Advanced Ecological Data Analysis taught at Rutgers University by Malin Pinsky and Rachael Winfree. (However, the only course-specific material is Section 4; the rest should be applicable to any reader.)

https://afredston.github.io/learn-git/learn-git.html

14.5 Modern Statistics for Modern Biology

Susan Holmes, Wolfgang Huber

The aim of this book is to enable scientists working in biological research to quickly learn many of the important ideas and methods that they need to make the best of their experiments and of other available data.

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

14.6 Orchestrating Single-Cell Analysis with Bioconductor

Aaron Lun, Robert Amezquita, Stephanie Hicks, Raphael Gottardo

This is the website for “Orchestrating Single-Cell Analysis with Bioconductor”, a book that teaches users some common workflows for the analysis of single-cell RNA-seq data (scRNA-seq).

https://osca.bioconductor.org/

14.7 Statistics in R for Biodiversity Conservation Paperback

by Carl Smith , Antonio Uzal , Mark Warren

A practical handbook to introduce data analysis and model fitting using R to ecologists and conservation biologists. The book is aimed at undergraduate and post-graduate students and provides access to datasets and RScript.

Paid product ~$10

https://www.amazon.co.uk/dp/B08HBLYHQL/ref=cm_sw_r_cp_apa_i_g0luFb86PXJ9Z

14.8 Numerical Ecology with R

by Daniel Borcard, François Gillet, Pierre Legendre

This new edition of Numerical Ecology with R guides readers through an applied exploration of the major methods of multivariate data analysis, as seen through the eyes of three ecologists. It provides a bridge between a textbook of numerical ecology and the implementation of this discipline in the R language. The book begins by examining some exploratory approaches.

eBook ~$60

https://www.springer.com/us/book/9783319714035

14.9 Introduction to Data Analysis with R

by Jannik Buhr

This is a video lecture series with accompanying lecture script that is designed to read much like a book. The lecture is held in English for biochemists at Heidelberg University, Germany, but the examples covered are no specific to life sciences in order to enable a focus on learning the techniques with R.

free

https://jmbuhr.de/dataIntro20/