#Bioinformatics
Showing 60 of 218 repositories tagged #bioinformatics, ranked by stars
List of Computer Science courses with video lectures.
Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 140 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.
Data Apps & Dashboards for Python. No JavaScript Required.
Official git repository for Biopython (originally converted from CVS)
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
A DSL for data-driven computational pipelines
Single-cell analysis in Python. Scales to >100M cells.
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Unix, R and python tools for genomics and data science
Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.
Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
Protein Graph Library
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
A plotly.js React component from Plotly 📈
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
A comprehensive library for computational molecular biology
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
Python library to facilitate genome assembly, annotation, and comparative genomics
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
🔬🦞 A self-evolving AI research colleague for scientists. 285 skills, zero hallucination, persistent memory.
Python package for graph neural networks in chemistry and biology
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Tools to process and analyze deep sequencing data.
Annotated data.
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
A Go package for engineering organisms.
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
Interactive network visualization in Python and Dash, powered by Cytoscape.js
Cell type annotation for single-cell RNA-seq using multi-LLM consensus
Gene cluster comparison figure generator
Yet another redundant workflow engine
ScienceClaw is a personal research assistant built with LangChain DeepAgents and AIO Sandbox infrastructure, adopting a completely new architecture beyond OpenClaw. It offers stronger security, better transparency, and a more user-friendly experience.
Quickly search, compare, and analyze genomic and metagenomic data sets.
BioMCP: Biomedical Model Context Protocol
An analysis and visualization platform for 'omics data
A curated list of resources for learning bioinformatics.
Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.
Genome assembly evaluation tool
Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.
A general, evolvable, and distributed agent framework & harness for data science.
Library for Digital Pathology Image Processing
CellRank: dynamics from multi-view single-cell data
Structural variant toolkit for VCFs
An open source platform for managing and analyzing biomedical big data
A genome visualization python package for comparative genomics
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
DANCE: a deep learning library and benchmark platform for single-cell analysis
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
Scikit-learn compatible library for molecular fingerprints and chemoinformatics
🧬 immunarch [R package] – Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
A genome browser designed for complex structural variants and long reads.
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Source code for JBrowse 2, a modern React-based genome browser