Lists (27)
Advancing Julia
Repos that advance Julia as a compelling scientific programming language.AI-Assisted Engineering
Programming will never be the same.Bioinformatics
"Bioinformatics is terrible. Everybody knows bioinformatics is terrible...it’s not a good situation that we’re in."Biology in the Frontend
Interactive simulations, visualizations, and demos served in the browser.Command-line Utilities
Future-facing command-line tools written in innovative languages or that raise the bar in some other way.Data Visualization
Know your data by seeing it.Design as Code
Functional Programming
Writing composable, refactorable, and robust code with an FP paradigmGenomic epidemiology🦠🧬
Get started in Bioinformatics
Looking for inspiration to get started with making sense of noisy biological data? These repos punch above their weight.GIS
Spatial statistics, cartography, and other spatially explicit methodsGleam is cool
Glimpses of Jai
Early looks at the Jai programming language, which remains in closed betaGo in Bioinformatics
Tools built in Go that can be interfaced with in the command line, or in Go source code.Learning Me a Haskell
Finally giving in and learning Haskell—I may never be the sameMetagenomics is hard :(
but fun?Python as a Glue Language
Python is beautiful...but slow. These tools help bring out its best side: as an elegant glue language connecting faster pieces of software.R in Science
"The best thing about R is it was designed by statisticians. The worst thing about R is it was designed by statisticians."Rust does all the things
Tools built in Rust that can be interfaced with in the command line, or in Rust source code.Scientific Reproducibility
Tools that make doing reproducible science—a very difficult task!—easier.Simulation & Testing
Software for Biodiversity
Software developed to help understand and solve the biodiversity crisis and advance our understanding of ecology and evolution in general.Standards for Excellent Programs
TUIs
I love TUIs and I don't care who knows itTurns out your app is a database
Repos that are explicitly--or accidentally--database projects.TypeScript Eats the World
We all give into TypeScript eventually...Workflow Orchestration
Tools for deploying many steps of dataflow across a variety of infrastructuresStars
🖼️ A command-line system information tool written in bash 3.2+
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
Github action to check for broken links in Markdown, HTML, and text files using lychee, a fast link checker written in Rust.
genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with advanced filters, detailed logs and reports, file integrity…
This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical metagenomic sequence data. Please download SURPI+ software …
🌱📦 A collection of bioinformatics tools for working with sequence data.
A simple CLI tool to get notified when a command is complete.
Omni-C data processing documentation and scripts