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The `TrIdent` R package automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.

Tools for detecting drug-protein interactions and estimating IC50 values from chemoproteomics data. Implements semi-parametric isotonic regression, bootstrapping, and curve fitting to evaluate compound effects on protein abundance.

Noodle is a public, read-only web application for semantic discovery and exploration of biomedical literature sourced from PubMed, Europe PMC, and OpenAlex. It accepts natural-language research questions and presents ranked publications together with gene, genetic variant, and phenotype views. Publication pages provide provenance, identifiers, source links, indexed concepts, and navigable semantic-neighbourhood graphs. The companion Noodle Biomedical Literature Discovery MCP exposes the same public discovery domain through a read-only, source-linked Model Context Protocol interface with bounded citation and semantic graph traversal. Semantic proximity, citation distance, co-mention, and search rank are discovery signals and do not establish scientific evidence, causality, diagnosis, or treatment.

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.

Polymathic AI's large omnimodal foundation model for astronomical surveys, seamlessly integrating 39 distinct data modalities including imaging, spectra, photometry, and catalog entries for similarity search, property prediction, and generative modeling across legacy surveys (MIT)

xgt is a command-line tool for programmatic access to the GTDB REST API. It provides four subcommands: search (genome queries with pagination), genome (cards, metadata, taxonomic history), taxon (lineage and genome set retrieval), and diff (per-rank taxonomic comparison between any two GTDB releases). All subcommands support batch input, JSON/CSV/TSV output, file splitting, and automatic retry. Implemented in Rust as a self-contained binary with no runtime dependencies.

Inflexa is an open-source, agentic orchestration platform for computational biology and translational medicine. It is designed to assist researchers in analyzing multi-omics, cheminformatics, and imaging data by reading published literature, designing multi-step analysis plans, and executing experiments with full reproducibility.

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.

Physics-informed neural networks in Julia

SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as "sssom:mapping_justification" are defined in the sssom namespace.

Deep learning software to decode EEG, ECG or MEG signals, providing standardized neural network models, preprocessing pipelines, and evaluation workflows for brain-computer interfaces and cognitive neuroscience research (1.2K+ stars, BSD 3-Clause, actively maintained)

The modern C++ library for sequence analysis.

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Free-text promptable universal 3D medical image segmentation foundation model enabling zero-shot segmentation of diverse anatomical structures and pathologies via natural language prompts across CT, MRI, and other volumetric imaging modalities (DKFZ, 195+ stars, Apache 2.0)

Python Materials Genomics: robust materials analysis library defining classes for structures and molecules with support for many electronic structure codes; foundational toolkit powering the Materials Project (Berkeley Lab, 1.8K+ stars)

Parallel Computing and Scientific Machine Learning: MIT 18.337J/6.338J course materials (1.9k+ stars)

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.

Open-source deep learning toolbox for bioimage analysis providing a unified, configuration-driven framework for 2D/3D semantic segmentation, instance segmentation, classification, denoising, super-resolution, and self-supervised learning; integrates state-of-the-art architectures including U-Net, Vision Transformers, and ConvNeXt, designed for microscopy and biomedical imaging researchers without extensive coding expertise (MIT License, actively maintained)

atomate2 is a library of computational materials science workflows.

RAiSD-AI is a tool for training, testing, and deploying Convolutional Neural Networks to detect selective sweeps in genomic data, extending the functionality of the original RAiSD software with machine learning capabilities. It supports SNP data processing, CNN model training with TensorFlow or PyTorch, and genome-wide selective sweep detection.

scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.

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.

A library of core preprocessing routines.

MiRA (Multilayer Interactive Rendering Application) is a free, browser-based, installation-free tool for interactive visualisation of multilayer networks in ecology and biology. While developed with biology in mind, MiRA can render any multilayer network. Available as a standalone web app and also fully integrated into the emln R package.

Segment Anything Model for microscopy: interactive and automatic segmentation of light, electron, and fluorescence microscopy images in 2D and 3D, with domain-specific fine-tuning workflows for scientific imaging (1.5K+ stars)

Provides an R interface for various subsampling algorithms implemented in python packages. Currently, interfaces to the geosketch and scSampler python packages are implemented. In addition it also provides diagnostic plots to evaluate the subsampling.

Chemical Information from the Web.

AI co-author covering the entire research lifecycle — from an under-specified research direction to a published paper; includes ResearchStudio-Idea for evidence-grounded research ideation and ResearchStudio-Reel for turning finished papers into posters, narrated videos, blogs, and interactive reels; runs as skills on Claude Code and Codex (1.2K+ stars, MIT License, 2026)

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.

Deep learning with spiking neural networks in Python, providing gradient-based training of SNNs via PyTorch autodifferentiation for brain-inspired computing and neuromorphic research, with online learning capabilities and extensive tutorials (1.9K+ stars, actively maintained)

GAIn is a platform for annotating genetic variants, genomic positions, and regions with reproducible, declarative pipelines using curated Genomic Resource Repositories.

Self-evolving AI scientist with 6 specialized sub-agents (plan/research/code/debug/analyze/write) and persistent memory, #1 on DeepResearch Bench II and AstaBench, supporting multi-provider LLMs and multi-channel deployment (Apache 2.0, 2026)

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)

Regional Association of Methylome variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify genome-wide Variable Methylated Loci (VML) from microarray DNA methylation data; then, using genomic and exposomic data, it can identify which model out of the following explains best the DNA methylation variability at each VML: genetic (G), environmental (E), additive (G+E) or interactive (GxE).

Curated open dataset collection of 602M+ observational and perturbational single-cell profiles for accelerating virtual cell model creation, integrating Tahoe-100M and scBaseCount data with Google Cloud Marketplace distribution (Arc Institute, 2025-2026)

Markerless pose estimation of user-defined features with deep learning for all animals including humans, enabling quantitative behavioral analysis in neuroscience and ethology (Nature Neuroscience 2018, 5.6K+ stars)

It is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc).

MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

Implements R bindings to C++ code for analyzing single-cell (expression) data, mostly from various libscran libraries. Each function performs an individual step in the single-cell analysis workflow, ranging from quality control to clustering and marker detection. Additional wrappers are provided for easy construction of end-to-end workflows involving Bioconductor objects like SingleCellExperiments.

FAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects. This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.

A much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.

Accessible protein design platform via Google Colab integrating AlphaFold2, RoseTTAFold, and ProteinMPNN for de novo hallucination, fixed backbone design, and binder design (Sergey Ovchinnikov, 2022+)

Offline-first scientific writing workspace powered by Claude, integrating LaTeX, Python, and 100+ scientific skills with local execution, Zotero integration, and privacy-focused design (2026)

Curated list of atomistic ML projects for materials science

Vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.

SOTA multimodal document parsing with 1.2B parameters outperforming GPT-4o, converts PDFs to LLM-ready Markdown/JSON