Manuals for commonly used lab software

Please add links here that you found useful while learning any software that we use in the lab frequently. Please remove or replace broken links.

The software tools listed at the top are more frequently in our lab, so it will be good to learn them first.

Emacs and Org Mode¶

Purpose: Word processor for writing lab notebook, fellowship applications, and manuscripts.

Absolute Beginner's Guide to Emacs
Using Emacs, Org-mode and R for Research Writing
See post on Emacs useful tips
Example of a fellowship written in Org Mode. Click on Raw to see the raw text.
Rasi's .emacs file has a set of configurations that are useful for our lab's workflow.

Purpose: Version Control

Purpose: Vector Graphics Editing

Purpose: File, directory, and software manipulation

Introduction to Bash
Unix and Linux: Visual QuickStart Guide – Basic but thorough introduction. Chapters 1–6 are particularly useful.

Purpose: Programming and Data Analysis

R for Data Science – Introduction to tidy data analysis principles. We use tidyverse R packages for almost all of our data analyses. So you will want to master the initial chapters (1–20) asap.
Sequences, Genomes, and Genes in R / Bioconductor – Quick overview of data structures in Bioconductor for Genomic Analysis by Martin Morgan. After you finish this, you can dig into the books by Rafael Irrizary or Kasper Daniel Hansen.
Rafael Irrizary's book for data analysis in life sciences – Comprehensive introduction to R packages we use in the lab.
Bioconductor for Genomic Data Science – Excellent and comprehensive introduction to deep sequencing analysis (includes short videos for each topic).
Sign up for the fredhutch.io mailing list and register for their classes on R. These classes fill up very fast so sign up right away.

Purpose: Writing Github issues

Purpose: Command-line Text Editor

Using Vim commands in Emacs through the Evil package can make your writing very efficient.

Interactive vim tutorial - good place to start
Practical Vim Book has useful tips once you are familiar with the basics of vim.

Purpose: Command-line tools for biological sequence analysis

Purpose: Bitmap Image Editing

Purpose: Word Processor, Spreadsheets

Purpose: Add / Delete / Change Pages in PDF files

Purpose: Stochastic simulations

Bioinformatics Data Skills - Book on Reproducible and Robust Research with Open Source Tools
Hackr.io - Share and discover the best programming tutorials and courses online.