a set of SKILLS.md for doing bioinformatics with agents like claude code

a snakemake pipeline to process ChIP-seq files from GEO or in-house

ROSE: RANK ORDERING OF SUPER-ENHANCERS

TF Binding and Expression Target Analysis 2

Django + Tailwind CSS = 💚

A curated list of best ai tools

Unified knowledge-driven network inference from omics data

Educational exploration of the DeepSeek-V3 Model Architecture

A user-friendly pipeline for viral diversity analysis and characterization.

SIGnature is a Python package that empowers researchers to rapidly query gene sets across diverse single-cell RNA sequencing (scRNA-seq) datasets through precomputed gene attribution scores.

A Python library for extracting structured information from unstructured text using LLMs with precise source grounding and interactive visualization.

Master programming by recreating your favorite technologies from scratch.

Curated list of project-based tutorials

Full stack, modern web application template. Using FastAPI, React, SQLModel, PostgreSQL, Docker, GitHub Actions, automatic HTTPS and more.

GPT4All: Run Local LLMs on Any Device. Open-source and available for commercial use.

Open source alternative to AWS. Elastic compute, block storage (non replicated), firewall and load balancer, managed Postgres, K8s, AI inference, and IAM services.

🔥 Clone and recreate any website as a modern React app in seconds

Analyzing cellular niches in spatial transcriptomics data

Integrative Composable Visualization Framework for ggplot2

CUT&RUN and CUT&Tag data processing and analysis

Cell types enrichment analysis

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

Brings bulk and pseudobulk transcriptomics to the tidyverse

Introduction to Snakemake for Bioinformatics

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping

Single-Cell Genotyping Tool

ENCODE Uniform processing pipeline for ChIP-seq