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pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

Gene expression prediction

DANTE is a software tool for genotyping and characterizing tandem repeats (TRs) from both second- and third-generation sequencing data. It supports the analysis of short-read massively parallel sequencing (sr-MPS) and long-read massively parallel sequencing (lr-MPS), enabling accurate repeat characterization across a wide range of loci. A key feature of DANTE is its ability to determine genotypes at nucleotide resolution, including the characterization and phasing of complex repeat motifs. For sr-MPS data, the tool determines allele size and sequence composition of alleles for which spanning reads are generated. In addition, it identifies alleles that exceed the sequencing read length by estimating their presence from partial read evidence and supports the visualisation of the sequence composition of partial reads. For lr-MPS data, where complete repeat regions are typically sequenced, DANTE determines the allele size and sequence composition of identified alleles.

GraphExperiment provides users and developers with an S4 class that extends `SingleCellExperiment` by offering infrastructure to store and retrieve networks (`igraph` objects) representing how assay features and/or observations are associated with each other. The class was designed to store networks inferred from high-dimensional quantitative data, with feature-feature networks including gene coexpression networks (GCNs), gene regulatory networks (GRNs), and co-abundance networks (from proteomics and metabolomics), and observation-observation network including cell-cell distances, species-species relationships, and sample-sample similarities.

Annotate a VCF with other VCFs/BEDs/tabixed files.

Provides C and C++ hdf5 libraries.

Cross-platform system optimizations for accelerating AlphaFold3 training with 1.73x speedup and 1.23x memory reduction

Learning the language of protein-protein interactions

Genomic foundation model for metagenomic and genome annotation, featuring an 8k base-pair context and 500M parameters trained on 386B base pairs of eukaryotic DNA; provides expert models and a unified CLI for prokaryotic/eukaryotic coding-sequence annotation with strong performance on Genomic Benchmarks, Nucleotide Transformer tasks, and custom Gener tasks (GenerTeam, 314+ stars, MIT License)

Automatic atomic model building program for cryo-EM maps using deep learning, enabling rapid de novo protein structure determination from electron density with high accuracy (3DEM/EMBL, 169+ stars)

Performs laboratory unit conversions across molarity, OD600 cell density, C₁V₁ dilution, and related dimensional pairs from mass, volume, molecular weight, and organism-specific OD factors. A browser calculator combines four modes in one tabbed workspace with compound MW lookup, species-aware OD uncertainty ranges, cross-tab chaining, and shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits conversion inputs and returns structured results and shareable run identifiers.

Functions helpful for LIBD deconvolution project. Includes tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results. Working to include DLPFC datasets.

Translates spectrophotometer and NanoDrop readings into mass and molar concentrations for dsDNA, ssDNA, ssRNA, and protein from a single anchor input, with optional sequence-specific nearest-neighbor extinction coefficients. A browser calculator supports bidirectional unit conversion, batch processing of up to ninety-six NanoDrop export rows, and A260/A280 purity interpretation with plain-language warnings; a REST API exposes converter, batch, and purity modes for scripted use. Calculator arithmetic is hosted remotely; API clients transmit parameters and return structured result fields and shareable run identifiers.

Calculates sequence-derived molecular properties and related laboratory planning outputs from FASTA and assay setup inputs. The tool supports sequence analysis for DNA, RNA, and protein entries, plus dilution and ligation calculation modes through one API-backed workflow. Programmatic use is available through a Python library and command-line interface that submit run payloads and return structured result objects.

Translates between centrifuge RPM and relative centrifugal force using rotor geometry, reporting g-force or speed at rmin, ravg, and rmax. Convert mode handles rpm_to_rcf and rcf_to_rpm with rotor presets or manual radii in mm; transfer mode maps a source RPM on one rotor to an equivalent target RPM at matched rmax RCF; batch mode processes multiple spin steps from CSV or row arrays. A browser calculator and a Python library with command-line interface submit the same parameters to the Pepkio Tools API and return structured results with optional methods text and safety warnings.

Derives cells per well and suspension pipette volumes for standard 6-, 12-, 24-, 48-, 96-, and 384-well plates from a hemocytometer stock count, trypan blue viability, and target seeding confluency, with QC flags for low viability and impractical transfers. A browser calculator supports interactive planning with cell-line presets; 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 plate tables and shareable run identifiers.

Constructs Punnett squares and offspring genotype and phenotype ratios for complete, incomplete, codominant, ABO multiple-allele, and sex-linked Mendelian crosses from parent genotypes, with step-by-step walkthroughs and reduced ratio output. A browser calculator provides live grids, textbook presets, PNG and SVG export, and shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits cross inputs and returns structured grids, ratios, walkthroughs, and shareable run identifiers.

Evaluates Hardy-Weinberg equilibrium for diploid loci with two to six alleles using chi-square and Guo-Thompson exact tests, inbreeding coefficient F, and plain-language verdicts from observed genotype counts, allele frequencies, or biallelic disease incidence. A browser calculator provides De Finetti plots, export, and Wright-Fisher simulation under selection, drift, mutation, and migration; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits genotype or simulation inputs and returns structured results and shareable run identifiers.

Performs batch four-parameter and five-parameter logistic regression on multi-compound concentration–response screens to estimate IC50, EC50, pIC50, Hill slope, and related potency metrics with per-compound QC grades. A browser calculator supports CSV upload, curve review, and figure export; 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 concentration–response data and returns structured fit results and shareable run identifiers.

Processes 96-well plate absorbance data through blank subtraction, regression fitting, and dilution correction to report sample concentrations with QC flags for BCA, Bradford, and ELISA workflows. A browser calculator supports interactive grid entry with CSV and PDF export; 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 plate layout and absorbance values and returns model comparison, per-sample concentrations, and shareable run identifiers.

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Generalist deep learning algorithm for cell and nucleus segmentation across diverse image types, with human-in-the-loop training (2.0) and one-click image restoration (3.0), 70K+ training objects (Nature Methods 2021/2022/2025)

The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.

Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.

The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

General-purpose deep learning backbone for molecular modeling

The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.

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.

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 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.

A swiss army knife for manipulating and editing PDB files.

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.

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.

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)