Bioinformatics
- Introduction to Bioinformatics and Computational Biology by Shirley Liu
- Applied Computational Genomics by Aaron Quinlan
- DIY.transcriptomics by Daniel Beiting
- The Biostar Handbook (2e) by Istvan Albert
- Next-Generation Sequencing Analysis Resources by Genomics Core at NYU CGSB
- Orchestrating Single-Cell Analysis with Bioconductor (Amezquita et al., 2019) [R]
- Best Practices for Spatial Transcriptomics Analysis with Bioconductor [R]
- Single-Cell Best Practices (Heumos et al., 2023) [Python]
- Glittr – Git Repositories with Bioinformatics Training Material
Bioinformatics Blogs
- RNA-Seq Blog: Transcriptome Sequencing Research & Industry News
- DNA Confesses Data Speakby Tommy Tang [R]
- Decoding Biology by Evan Peikon [Python]
Bioinformatics YouTube Channels
- chatomics by Tommy Tang [R]
- Bioinformagician by Khushbu Patel [R]
- Sanbomics by Mark Sanborn
Bioinformatics Online Forums
- BioStars: An Online Q & A Resource for the Bioinformatics Community (Parnell et al., 2011)
- SEQAnswers: The next-generation sequencing community
- Bioinformatics Stack Exchange
- Reddit’s Bioinformatics Community: A subreddit dedicated to bioinformatics, computational genomics, and systems biology
R
- Harvard CS50’s Introduction to Programming with R by Carter Zenke
- R for Data Science (2e) by Hadley Wickham, Mine Cetinkaya-Rundel, and Garrett Grolemund
- ggplot2: Elegant Graphics for Data Analysis (3e) by Hadley Wickham
- Data Wrangling and Visualization with R by Rafael Irizarry
- Statistics and Prediction Algorithms Through Case Studies by Rafael Irizarry
- Tidy Modeling with R by Max Kuhn and Julia Silge
- Bioconductor: Open source software for Bioinformatics (Gentleman et al., 2004; Huber et al., 2014; Amezquita et al., 2020).
- Tidyomics: Open project to create tidy analysis packages for omics data (Hutchison et al., 2024).
- Dan MacLean (2019). R Bioinformatics Cookbook (Packt Publishing).
- Computational Genomics with R by Altuna Akalin
- RDocumentation: Search all R packages and functions on CRAN and Bioconductor
- Tidyverse Blog by Posit
- R-bloggers: R news and tutorials contributed by hundreds of R bloggers
Python
- Harvard CS50’s Introduction to Programming with Python by David J. Malan
- Polars: A lightning-fast dataframe package for data wrangling. If Pandas df is required for downstream analyses,
df.to_pandas()will do the trick. - Python for Data Analysis (3e) by Wes McKinney
- NumPy: The fundamental package for scientific computing in Python
- plonine: A faithful port of R’s famous ggplot2 graphing library to Python based on a grammar of graphics.
- scverse: A consortium of foundational tools for analysis of omics data in life sciences (Virshup et al., 2023).
- Biopython: A set of freely available tools for biological computation (Cock et al., 2009).
- Tiago Antao (2022). Bioinformatics with Python Cookbook - Third Edition (Packt Publishing).
- Biotite: A comprehensive library for computational molecular biology (Kunzmann et al., 2018, 2023).
- BioNumpy: Python library for array programming on biological datasets (Rand et al., manuscript).
- Rosalind: A platform for learning bioinformatics and programming through problem solving.
Unix
- Why Should Biologists Learn Unix for Bioinformatics? by NIH
- The Unix Workbench by Sean Kross
- The 50 Most Popular Linux & Terminal Commands - Full Course for Beginners by freeCodeCamp
- Learning Awk Is Essential For Linux Users by DistroTube
- Understanding Awk by Adam Gordon Bell
- Learning Sed Is Beneficial For Linux Users by DistroTube
Maths & Stats
- Statistics for Biologists by Nature
- StatQuest by Josh Starmer
- Statistical Inference via Data Science–A ModernDive into R and the Tidyverse by Chester Ismay and Albert Y. Kim [R]
- An Introduction to Statistical Learning by Gareth James, Daniela Witten, Trevor Hastie, Rob Tibshirani, and Jonathan Taylor [R & Python]
- ISLR tidymodels labs by Emil Hvitfeldt [R/Tidymodels]
- Khan Academy by Sal Khan
- 3Blue1Brown by Grant Sanderson