scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

An extremely fast Python package and project manager, written in Rust.

Nextflow training material

Tips for Nextflow and cheatsheet for channel operation

A curated list of awesome Bioinformatics libraries and software.

A collection of awesome bio-foundation models, including protein, RNA, DNA, gene, single-cell, and so on.

Neural Networks: Zero to Hero

PyTorch Tutorial for Deep Learning Researchers

scRNAseq analysis notes from Ming Tang

A toolkit of spatial transcriptomic analysis.

Spatiotemporal modeling of spatial transcriptomics

This repository will host a (continously updated) list of various deep learning methods used in different stages of spatial transcriptomics analysis.

EPFL Course - Optimization for Machine Learning - CS-439

All Algorithms implemented in Python

Bioinformatics with Python Cookbook, Third Edition

Master the command line, in one page

A curated list of awesome command-line frameworks, toolkits, guides and gizmos. Inspired by awesome-php.

CellRank: dynamics from multi-view single-cell data

Table of software for the analysis of single-cell RNA-seq data.

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

collected resource for scRNA-seq analysis

Panoramic stitching of single cell data

Bioinformatics one liners from Ming Tang

Collection of bioinformatics training materials

Useful bash one-liners for bioinformatics.

Implement a ChatGPT-like LLM in PyTorch from scratch, step by step

Machine Learning From Scratch. Bare bones NumPy implementations of machine learning models and algorithms with a focus on accessibility. Aims to cover everything from linear regression to deep lear…

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

Curated (meta)list of resources for Biology.