A Collection of Useful Resources

R General:

• R For Data Science
• fasteR
• The R Inferno
• Advanced R 2nd Edition
• Advanced R 1st Edition
• Mastering Shiny
• Production Grade Shiny Apps
• R Packages Book

Bioinformatics:

• DESeq2 workflow
• edgeR workflow
• csaw book for CHIP/ATAC seq
• Orchestrating Single cell Analysis with Bioconductor
• Single Cell Best Practices book
• Guide to creating design matrices
• Orchestrating Microbiome Analysis in R
• QIIME2 for microbiome analysis
• Bioconductor Awesome Lists
• ATAC-seq pipeline
• Intro to RNAseq
• Fred Hutch Bioinfo Primer book
• Analyzing CRISPR screens with edgeR

Statistics:

• Modern Statistics for Modern Biology: I use this all the time
• Statistical Rethinking: Highly recommend
• Regression and Other Stories: Read this book
• What does a statistical method assume: Read this blog
• Andrew Gelman’s Blog
• Regression Modeling Strategies Course Notes
• Biostatistics for Biomedical Research
• introduction to modern statistics
• The basics of bayesian statistics
• Hidden Markov Models in R
• Review of recommendations for variable selection
• Imputation methods
• How to read PCA plots

Programming general:

• Advanced Bash scripting (old http link)
• minimal safe bash script template
• Effective Shell
• Software Carpentry on Automation and Make
• Modern C
• Assembly Language
• Programming Paradigms: watch this and you’ll understand how programming generally works
• GNU C Language manual

Mathematics:

• Understanding Mathematics
• Programmer’s introduction to mathematics
• Math pronunciation guide

ML/AI:

• Generative AI for beginners
• Understanding Deep Learning
• Google ML Course

Misc:

• Papers We Love
• For Better Science
• Bionumbers
• chmod calculator you’d be surprised how often you use this
• Online encyclopedia of integer sequences

Bio Art : free SVGs to create diagrams:

• inkscape For creating the diagrams
• NIH BioArt
• bioicons
• Open Science Art
• Scidraw
• Reactome Icon Library
• Smart Servier Medical Art