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Access to Biological Web Services from Python.

Universal foundation model for grounded biomedical image interpretation, enabling comprehensive visual understanding, reasoning, and grounding across diverse biomedical imaging modalities with strong zero-shot generalization (55+ stars, Apache 2.0, 2025-2026)

Implementation of the Ibex algorithm for single-cell embedding based on BCR sequences. The package includes a standalone function to encode BCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects.

Geneset Ordinal Association Test Enrichment Analysis (GOATEA) provides a 'Shiny' interface with interactive visualizations and utility functions for performing and exploring automated gene set enrichment analysis using the 'GOAT' package. 'GOATEA' is designed to support large-scale and user-friendly enrichment workflows across multiple gene lists and comparisons, with flexible plotting and output options. Visualizations pre-enrichment include interactive 'Volcano' and 'UpSet' (overlap) plots. Visualizations post-enrichment include interactive geneset dotplot, geneset treeplot, gene-effectsize heatmap, gene-geneset heatmap and 'STRING' database of protein-protein-interactions network graph. 'GOAT' reference: Frank Koopmans (2024) <doi:10.1038/s42003-024-06454-5>.

gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.

A tool and library for creating quantum chemistry input files.

by Fabian-Robert Stöter.

Data analysis for Single File Injections(SFIs) mode LC-MS analysis. In SFIs mode, pooled samples are initially injected to serve as reference peaks for subsequent analyses. Repeated injections of individual samples are then performed at fixed time intervals using isocratic elution. This package provides the functions to analyze data from SFIs mode including peak picking and peak reassignment.

Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <doi:10.1093/bioinformatics/btq706>.

A comprehensive R package for identifying and ranking influential nodes in biological and other complex networks. The package implements the Integrated Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR), SIRIR, and numerous network centrality measures, enabling network topology analysis, influential node detection, feature prioritization, and candidate biomarker discovery. It also provides functions for network reconstruction, centrality assessment, visualization, and analysis of relationships between centrality measures.

A Swiss Army knife for genome arithmetic.

Sparse identification of nonlinear dynamics

BatchSVG is a method to identify batch-biased spatially variable genes (SVGs) in spatial transcriptomics data. The batch variable can be defined as sample, donor sex, or other batch effects of interest. The BatchSVG method is based on the binomial deviance model (Townes et al, 2019).

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

Closed-loop multi-agent system from hypothesis to verification across 12 scientific tasks, #1 on MLE-Bench (36.44%)

A swiss army knife for manipulating and editing PDB files.

A Go library and command line utility for engineering organisms.

Calculate mass, elemental composition, and mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence.

A static web application presents an interactive knowledge graph of single-cell long-read RNA sequencing literature synthesized from seven source papers. Users navigate mind-tree, network graph, guided learning-path, and Sankey views linking platforms, protocols, methods, and software. A benchmark tab provides 34 question-answer pairs with category and difficulty filters, exportable as JSON or CSV for LLM and agent evaluation.

Phylo-Movies is an open-source React and Flask web application, also available as a desktop app, for inspecting ordered phylogenetic tree series. It computes and visualizes subtree-prune-and-regraft transition frames between consecutive trees, helping users see which taxa or subtrees move across sliding-window analyses, bootstrap replicates, and curated tree-series comparisons. The viewer includes timeline playback, tree comparison, MSA context, coloring, analytics, image export, and recording tools.

Databank of optimised macromolecular structures. PDB-REDO entries are refined, rebuilt and validated with one consistent protocol using the equivalent entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically have higher structural quality and a better fit to the experimental data.

The European Genome-phenome Archive (EGA) provides long-term storage and controlled sharing of personally identifiable genetic data. The Rega package offers a streamlined and extensible R interface to the EGA API, facilitating the programmatic upload of metadata. GEO-like Excel submission template is provided as a default method of organizing submission metadata.

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

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.

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet).

Lifecycle-Aware Memory (LAM) primitive and benchmark for long-horizon research agents, achieving 65.95% mean reproduction on PaperBench and 94.66% on SurveyBench through Capital Chunk Memory (CCM) with versioned content, structural multi-hop relevance, and provenance-grounded composition; 10 peer-reviewed acceptances at FSE/ICML/TOSEM/AEI/ICoGB (1.3K+ stars)

Programmatic data labeling and weak supervision

Multi-agent system with Parser-Planner-Painter architecture converting `paper.pdf` to editable `poster.pptx`, outperforms GPT-4o with 87% fewer tokens

An interface to the community supported database for amino acid/protein modifications using mass spectrometry.

The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

Self-evolving AI research colleague built on OpenClaw with 285+ runtime-adaptive skills across 28+ disciplines, persistent cross-session research memory, and zero-hallucination citation protocols; agent autonomously writes new SKILL.md files based on research patterns without redeployment (828+ stars, MIT License, 2026)

D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.

Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Concatenation software for the fast assembly of multi-gene datasets with character set and codon information.

Estimates PCR primer melting temperatures and polymerase-specific annealing temperatures from sequence and buffer inputs, with per-pair QC for hairpins, dimers, and Tm balance. A browser calculator supports interactive single-pair and batch entry (up to 200 pairs) with method comparison and export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic for the API client is hosted remotely; sequences are transmitted for programmatic runs while the web interface performs calculations in the browser.

Computes weighed laboratory buffer recipes from target pH, concentration, and volume, accounting for separate preparation and working temperatures when pKa shifts with temperature. Supports calculator mode from dry reagents and stock dilution mode, returning acid and base masses, ionic strength estimates, optional NaCl adjustment, gravimetric and titration routes, and stepwise protocols. A browser calculator supports interactive recipe entry with shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured recipe tables, compatibility warnings, and shareable run identifiers.

Plans PCR and qPCR master-mix reagent volumes from stock and final concentrations, reaction counts, and pipetting overage, with consolidated totals when several assays are prepared together. A browser calculator supports interactive recipe entry with printable bench sheets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured volume tables, dilution warnings, and shareable run identifiers.

Computes laboratory solution preparation parameters—powder mass to weigh, stock and diluent volumes for single dilutions, and multi-step serial concentration tables—with correction for hydrated salts and supplier purity. A browser calculator supports interactive prep planning with saved recipes and shareable links; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured protocol steps and shareable run identifiers.

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Family of causal genomic foundation models trained on 1T tokens (~6T DNA base pairs) from the Carbon Pretraining Corpus, combining eukaryote genes, mRNA transcripts, and prokaryote genomes with a hybrid text/6-mer tokenizer; Carbon-3B matches or beats Evo2-7B on zero-shot DNA evaluations including sequence recovery, variant effect prediction, and perturbations (Apache 2.0, 201+ stars)

Provides `dplyr` verbs (`mutate`, `select`, `filter`, etc...) supporting `S4Vectors::DataFrame` objects. Importantly, this is achieved without conversion to an intermediate `tibble`. Adds grouping infrastructure to `DataFrame` which is respected by the transformation verbs.

This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.

Plans geometric serial dilution series for molecular biology and biochemistry workflows, rounding transfer volumes to declared pipette ranges and optional 96- or 384-well plate layouts. A browser calculator supports interactive protocol design; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured step tables and shareable run identifiers.

PathMED is a collection of tools to facilitate precision medicine studies with omics data (e.g. transcriptomics). Among its funcionalities, genesets scores for individual samples may be calculated with several methods. These scores may be used to train machine learning models and to predict clinical features on new data. For this, several machine learning methods are evaluated in order to select the best method based on internal validation and to tune the hyperparameters. Performance metrics and a ready-to-use model to predict the outcomes for new patients are returned.

State-of-the-art RNA 3D folding model developed with Stanford Das Lab and Kaggle competition winners, featuring a 488M-parameter AF3-like architecture with MSA and template-based modeling, enabling structure-driven drug discovery and RNA therapeutics design (NVIDIA-Digital-Bio, Apache 2.0)

This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

LLM-native molecular language that represents molecules as explicit graph-based code, enabling LLMs to operate and reason on chemistry directly with 5× lower token cost and ~76-80% accuracy on novel molecules vs ~20% for SMILES; supports small molecules, polymers, and Markush structures with lossless RDKit interconversion and Claude Code/Codex agent skills (AtomFlow, arXiv:2605.16480, 281+ stars, MIT License, 2026)

Foundation model for universal cell segmentation achieving state-of-the-art performance across bacteria, tissue, yeast, cell culture, and diverse imaging modalities (brightfield, fluorescence, phase), with pip-installable inference and Napari plugin (vanvalenlab/Caltech, bioRxiv 2024)

'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.

Apache 2.0 single-cell foundation model family scaling to 3B parameters, pretrained on 266M cell profiles including perturbation data and released with training, embedding, and downstream benchmarking workflows for disease-relevant single-cell tasks (2025)