Bench to Insights
Practical bioinformatics and data science guides for scientists who want to make the most of their data.
Linux command lineUbuntu, the filesystem, files, pipes, text processing, shell scripts, and SSH.
Git and version controlWhy it matters, the basics, branching and merging, and GitHub for scientists.
Containers with PodmanWhat containers are, building images, running them, volumes, networking, and Compose.
Programming with RVariables, data structures, control flow, functions, packages, tidyverse, and S4 classes.
Programming with PythonVariables, data structures, control flow, functions, packages, pandas, and polars.
ReproducibilityWhy it matters, Nextflow and nf-core, AWS Batch, real RNA seq runs, and Snakemake.
LLM assisted codingWhy coding agents matter, choosing one, configuring the main CLIs, and common pitfalls.