Find open-source science resources

Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

lcmsPlot is an R package designed for visualising Liquid Chromatography-Mass Spectrometry (LC-MS) data with publication-ready high-quality plots. The package enables users to generate and customise chromatograms, mass traces, spectra, and more with fine-tuned aesthetics and annotation options.

Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.

Open-source LLM-powered R&D agent framework automating data-driven AI solution building through automated research, development, and evolution; achieves top open-source performance on MLE-Bench with dual Researcher-Developer agents and supports research copilot, data mining, Kaggle, and quant R&D workflows (13.6K+ stars, MIT License, 2025-2026)

Analysis of molecular dynamics trajectories.

ProtSent-V2 35M plus one more contrastive pass on a fresh draw of the corpus, with a DMS/ProteinGym CoSENT target and a Global Orthogonal Regularization term added.

SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.

High-performance molecular simulation toolkit

Open-source, local-first desktop AI research workbench for scientific computing with Python/R, MCP bioinformatics tools, SSH/WSL/GPU runtimes, and OpenAI/Anthropic models (857+ stars, 2026)

PyTorch domain library for geospatial deep learning providing standardized datasets, samplers, transforms, and pre-trained models for remote sensing, land cover mapping, and environmental monitoring (Microsoft, 4K+ stars)

Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.

dadi is a bioinformatics tool for inferring demographic history and selection from genetic data using diffusion approximations, offering speed and flexibility in modeling population dynamics. It supports up to three populations with customizable parameters and provides efficient computational performance.

Neuro-imaging file formats.

The R package decemedip is a novel computational paradigm developed for inferring the relative abundances of cell types and tissues measure by methylated DNA immunoprecipitation sequencing (MeDIP-Seq). This paradigm allows using reference data from other technologies such as microarray or WGBS.

Python package for segmenting geospatial data with the Segment Anything Model (SAM), enabling zero-shot object segmentation in satellite and aerial imagery for remote sensing and Earth observation (MIT, 4k+ stars)

Scalable genomic analysis.

Agent skill for AI-assisted scientific manuscript writing review distilled from Stanford's *Writing in the Sciences* course, performing five sequential editorial audit passes on clarity, voice, structure, consistency, and integrity (2026)

MCP server enabling spatial transcriptomics analysis via natural language, integrating 60+ methods including SpaGCN, Cell2location, LIANA+, CellRank for Visium, Xenium, MERFISH platforms

Probabilistic framework for inferring cell fate decisions and trajectory dynamics from multi-view single-cell data using Markov chains and machine learning, integrating RNA velocity, pseudotime, and metabolic labeling to predict differentiation paths and terminal states (scverse/Theis Lab, 449+ stars, BSD 3-Clause)

Microsoft AI for Good Lab's open-source biodiversity research hub providing AI models, edge devices, and tools for wildlife monitoring and conservation, including MegaDetector (camera trap animal detection), SPARROW (species recognition), PytorchWildlife (conservation AI toolkit), and bioacoustics analysis pipelines (1K+ stars)

Research coding benchmark curated by scientists with 338 subproblems across 16 subdomains (physics, math, materials, biology, chemistry), evaluating LLMs on realistic scientific programming tasks with gold-standard solutions (NeurIPS 2024)

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyse your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.

Curated, accuracy-first collection of benchmarks for evaluating LLMs on scientific reasoning and discovery across mathematics, physics, chemistry, materials science, biology, and agentic science (subinium, 29+ stars, MIT License, 2026)

The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/).

GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.

Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.

BIOSZEN is an open-source R package and modular Shiny application for reproducible analysis and visualization of experimental biological data from Excel or CSV files. It supports statistical testing, control-based normalization, replicate-aware quality control, and customizable scientific plots. Its microbial growth-curve module analyzes optical-density time series and automatically extracts quantitative growth parameters, including maximum specific growth rate (µMax), doubling time, lag time, maximum optical density (ODmax), time to maximum growth, area under the curve (AUC), and initial optical density (OD0). Results can be exported as processed datasets, statistical summaries, analysis metadata, scientific graphics, and editable PowerPoint figures.

Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data. HPAanalyze is designed to fullfill 3 main tasks: (1) Import, subsetting and export downloadable datasets; (2) Visualization of downloadable datasets for exploratory analysis; and (3) Working with the individual XML files. This package aims to serve researchers with little programming experience, but also allow power users to use the imported data as desired.

A DINOv2 ViT-S/14-reg fine-tuned so that an image of a molecular structure diagram embeds where its molecule embeds in the frozen MIST-28M embedding space. Objective: smooth-L1 regression onto the frozen target, no negatives (the JEPA move).

A DINOv2 ViT-S/14-reg fine-tuned so that an image of a molecular structure diagram embeds where its molecule embeds in the frozen MIST-28M embedding space. Objective: SigLIP sigmoid pairwise loss.

Text-space optimizer that treats agent skill documents as trainable parameters for frozen LLMs, using scored rollouts and held-out validation gates to iteratively improve reusable natural-language skills; includes SkillOpt-Sleep for nightly self-evolution and improves accuracy across Claude Code, Codex, Copilot, and direct-chat harnesses, making it a meta-tool for evolving scientific agent skill workflows (15.5K+ stars, MIT License, PyPI)

AI-powered note linking and research graph navigation

ReviewAid is an open-source AI-assisted tool for full-text screening and data extraction in systematic reviews. It supports evidence synthesis workflows by using large language models to classify articles according to user-defined PICO criteria and extract structured information from full-text publications. ReviewAid is designed as a supplementary reviewer rather than a replacement for human judgement. It aims to reduce manual workload, improve consistency, and assist researchers during screening and data extraction while maintaining human oversight throughout the evidence synthesis process.

PyTorch toolkit for deep neural networks in atomistic simulations, implementing SchNet, DimeNet++, PaiNN, and GemNet for molecular dynamics and quantum chemistry (900+ stars)

NOS-TLPlot is an open-source tool for visualizing Newcastle–Ottawa Scale (NOS) risk-of-bias assessments in systematic reviews. It converts NOS star ratings into publication-ready traffic-light plots and 12 specialized visualizations, enabling reviewers and readers to interpret study-level risk-of-bias results clearly and reproducibly.

RejuvenationKit is an open-source Python toolkit for reproducible auditing and analysis of longitudinal preclinical rejuvenation studies. It provides protocol-aware missingness checks, experimental-confounding diagnostics, attrition and analysis-readiness profiling, covariance-aware multichannel change detection, sequential response monitoring, randomized longitudinal inference, visualization, and integrity-tracked report bundles.

Unified interface for local, global, gradient-based and derivative-free optimization (800+ stars)

This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.

A vocabulary used in tandem with SHACL for representing node shapes

Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.

Aggregate results from bioinformatics analyses across many samples into a single report.

AI coding agent skills for KiCad electronics design that turn Claude Code, Codex, Gemini CLI, and other coding agents into full electronics design assistants; parses schematics and PCB layouts, builds power trees, audits connectors/ESD protection, validates passive networks, runs SPICE simulation, sources components from major distributors, and prepares boards for fabrication (aklofas, 974+ stars, MIT License, 2026)

bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations.