A Little Book of R for Bioinformatics

A beginner course from the National Cancer Institute that takes you from your first Unix commands to a full RNA-Seq analysis and pathway interpretation. No prior coding experience needed.

Alexandra L. Emmons and Joe Wu

Learn to work with DNA and RNA sequences using Python, Biopython, and the command line. Covers file formats, sequence alignment, genome browsers, and next-generation sequencing data.

David A. Hendrix

The official guide to Biopython, packed with ready-to-use code for reading sequence files, running BLAST, querying NCBI databases, and working with protein structures and phylogenies.

Jeff Chang, Brad Chapman, Peter Cock et al.

The open textbook of an MIT course on the algorithms behind genomics. Covers sequence alignment, hidden Markov models, gene finding, regulatory networks, and molecular evolution.

Manolis Kellis