Find open-source science resources

A local command-line tool for ancestral sequence reconstruction with gap-state inference using IQ-TREE. It supports nucleotide, amino acid, and codon sequence alignments and reports site-wise posterior probabilities of ancestral states.

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

RiSPICE (Rice SNP Prioritization Integrating Chromatin Effects) is a computational framework for prioritizing non-coding rice variants by integrating predicted chromatin effects from a fine-tuned DNA language model.

AI-driven desktop workbench for computational materials science with an interactive 3D structure editor, natural-language CatBot assistant, visual DAG workflow engine, remote-cluster access, and HPC job submission for VASP, ORCA, CP2K, Quantum ESPRESSO, GPAW, DFTB+, SIESTA, and LAMMPS (172+ stars, AGPL-3.0, 2026)

REFUTE is an open benchmark for scientific critique honesty and epistemic calibration on recent life-science and biomedical literature. It tests whether models keep claims inside what the evidence allows (overclaim / planted-flaw / falsifier selection) and whether stated confidence is calibrated, with judge-free MCQ axes plus open-ended critique scoring.

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.

netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.

Nallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly, and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional consequences.

197 bioinformatics and life science skills for Claude Code and AI agents, achieving 92.0% accuracy on BixBench. Covers RNA-seq, single-cell analysis, drug discovery, proteomics, and more. Powers OmicsHorizon (195+ stars, 2026)

Deep learning package for many-body potential energy representation and molecular dynamics, achieving quantum-mechanical accuracy with classical MD efficiency (DeepModeling, Gordon Bell Prize 2020, 1.9k+ stars)

Chemical reaction network and systems biology interface for scientific machine learning (SciML), enabling high-performance, GPU-parallelized simulation and analysis of complex biochemical systems with O(1) solvers (SciML, 518+ stars, Julia)

Developer toolkit for accelerating training and inference for AI in chemistry and material science, providing optimized GPU-accelerated workflows for molecular and materials machine learning (NVIDIA, 2026)

Python astronomy tools

Differentiable tokamak core transport simulator for fusion energy research, coupling PDE solvers with JAX auto-differentiation and neural-network surrogates for fast forward modelling, pulse-design, and trajectory optimization (Google DeepMind, Apache 2.0)

This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.

Democratizing AI scientists by transforming any LLM into research systems with 600+ scientific tools (Harvard MIMS)

Create and plot diffusion maps.

Curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines, enabling reproducible social science research with AI agents (Stanford REAP & CoPaper.AI, 3K+ stars, 2026)

Scientific taste learning framework showing AI can judge and propose research ideas with long-term impact; trains Scientific Judge as a generative reward model and Scientific Thinker as an ideation policy using Reinforcement Learning from Community Feedback (RLCF) on large-scale citation signals, with SciJudgeBench and released HuggingFace model weights (425+ stars, Apache 2.0, 2026)

A toolbox for machine learning in seismology, providing unified interfaces for deep learning seismic phase picking, earthquake detection, and waveform analysis across multiple benchmark datasets and pretrained models (397+ stars, actively maintained)

A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

Deep probabilistic framework for single-cell and spatial omics analysis, integrating scVI, scANVI, totalVI and other VAE-based models for batch correction, cell annotation, multi-omics integration, and RNA velocity (scverse/NumFOCUS, Nature Methods 2018/2024)

This package provides a convenient way to access the LINCS Signatures available in the iLINCS database. These signatures include Consensus Gene Knockdown Signatures, Gene Overexpression signatures and Chemical Perturbagen Signatures. It also provides a way to enter your own transcriptomic signatures and identify concordant and discordant signatures in the LINCS database.

Workflow optimized for the analysis of rare diseases, designed to detect SNVs, INDELs , CNVs and SVs in targeted sequencing data (CES/WES) and whole genome sequencing (WGS), built on Nextflow and following nf-core standards. It has an advanced variant annotation optimized for rare diseases diagnosis and discovery.

Auto-generates clean, customizable academic CVs from open research data (OpenAlex, ORCID, Crossref, DataCite, Open Editors Plus). A single canonical CV object drives every output format (HTML, PDF, DOCX, LaTeX, Markdown); citations render through CSL; and the account holder is matched by persistent identifier (ORCID / OpenAlex ID) rather than name string. Free for individuals, open-source, and FAIR by design.

Another cross-platform, efficient, practical and pretty CSV/TSV toolkit.

An interactive structure/property explorer for materials and molecules.

Visualization intermediate language that lets AI agents create expressive, polished charts from simple, human-editable specs, compiling the same input to 30+ chart types across Vega-Lite, ECharts, and Chart.js with an MCP server for agent integration (1.9K+ stars, MIT License, 2026)

Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

Robust, lightweight infrastructure for multi-agent autonomous self-evolution, built for autoresearch; agents run in isolated git worktrees, share knowledge through a common state directory, and are scored by a grader daemon; natively integrated with Claude Code, Codex, Cursor Agent, OpenCode, and Kiro (672+ stars, Apache 2.0)

Comprehensive collection of 125+ ready-to-use scientific skill modules for Claude AI across bioinformatics, cheminformatics, clinical research, ML, and materials science

Physics-Informed Neural networks for Advanced modeling in PyTorch

Benchmark evaluating AI agents on complex real-world scientific workflows in terminal environments across life, physical, earth, and mathematical sciences; featured on model cards for Claude Opus 4.7, GPT-5.5, and Gemini 3.1 Pro (200+ stars, Apache 2.0)

A Simulation Tool for Fractured and Deformable Porous Media.

Language agent gymnasium for challenging scientific tasks including DNA manipulation, literature search, and protein engineering

High-performance symbolic regression for discovering interpretable scientific equations from data, multi-population evolutionary search with Python/Julia backend, widely used in physics and astronomy (Cambridge, NeurIPS 2023)

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).

NVIDIA and King's College London's open-source AI toolkit for healthcare imaging, providing foundational frameworks for medical image annotation (MONAI Label), training (MONAI Core), and deployment (MONAI Deploy) across radiology, pathology, and endoscopy (8K+ stars, Apache 2.0)

JCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Principle-first scientific idea discovery framework that extracts reusable principles from public literature and private research materials, composes them into traceable Idea Cards with prior-art comparisons, and exports validation-ready research packs; emphasizes inspectable scientific objects, risk disclosure, and falsification paths (ICML 2026, 411+ stars, MIT License)

High-performance ML research

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

Molecular dynamics in JAX

Comprehensive Claude Code skill suite covering the full academic pipeline from deep research and paper writing to multi-perspective peer review, revision, and finalization; features multi-agent teams, PRISMA systematic review, style calibration, claim-level citation audits, integrity gates, and human-in-the-loop safeguards (38K+ stars, CC BY-NC 4.0, 2026)

Official Jupyter extension with `%%ai` magic commands and sidebar chat assistant, connecting multiple model providers and local inference

Scikit-learn compatible tabular foundation model for zero-shot classification and regression on mixed-type tabular datasets via in-context learning; applicable to diverse scientific datasets (1.8K+ stars, Apache 2.0)

High-accuracy RAG for scientific PDFs with citation support, agentic RAG, and contradiction detection