A Hitchhiker's Guide to Bioinformatics Analysis

A compilation of tutorials, books, and vignettes covering different topics in bioinformatics analysis.

During my journey as a bioinformatician, I often relied on well-written materials that helped me understand the available tools and methods and their applicability to different biological problems. This repository is an effort to share these resources and help other researchers navigate the intricacies of bioinformatics analysis. Hopefully, it will also make it easier to find those planning charts that have been sitting at the local planning department in Alpha Centauri for years.

Don't Panic!

R

RStudio Education https://education.rstudio.com/

R for Data Science https://r4ds.hadley.nz/

Happy Git and GitHub for the useR https://happygitwithr.com/

Statistics

Michael Love's teaching notes https://mikelove.github.io/pages/teaching.html

Common statistical tests are linear models https://lindeloev.github.io/tests-as-linear/

An Introduction to Statistical Learning https://www.statlearning.com/

Bulk RNA-seq analysis

A guide to creating design matrices for gene expression experiments https://f1000research.com/articles/9-1444

Linear Models for Microarray and RNA-Seq Data User’s Guide https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

edgeR User's Guide https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

Analyzing RNA-seq data with DESeq2 https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Single-cell analysis

Single-cell best practices https://www.sc-best-practices.org/preamble.html

Orchestrating Single-Cell Analysis with Bioconductor https://bioconductor.org/books/release/OSCA/

Seurat vignettes https://satijalab.org/seurat/articles/

Microbiome analysis

phyloseq: Explore microbiome profiles using R https://joey711.github.io/phyloseq/

Introduction to the microbiome R package https://microbiome.github.io/tutorials/

Miscellaneous

Computational Genomics with R https://compgenomr.github.io/book/

Specific analysis and Visualizations

From Data to Viz https://www.data-to-viz.com/

Plotting PCA (Principal Component Analysis) https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_pca.html

Heatmaps https://jokergoo.github.io/ComplexHeatmap-reference/book/

GSEA + ORA https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Feature selection with Lasso models https://glmnet.stanford.edu/