Browse Tools

Open Targets Genetics — EMBL-EBI/Open Targets portal for GWAS-driven gene prioritisation via Locus-to-Gene (L2G) scoring, fine-mapping, and colocalisation analysis. Query variant-to-gene links, study

P2Rank — fast machine learning tool for predicting ligand binding sites from protein structure. Uses random forest classifier on physicochemical and geometric features of solvent-accessible surface po

PAGA (Partition-based Graph Abstraction) — trajectory inference and topology analysis for single-cell RNA-seq data. Computes a coarse-grained graph of cell clusters (PAGA graph) that captures connecti

Use when registering or co-aligning multiplexed whole-slide images (WSI) from the same FFPE tissue section with different IHC or immunofluorescence stainings. Covers piecewise affine alignment of OME-

PanglaoDB — curated single-cell RNA sequencing database providing cell type marker genes, scRNA-seq datasets, and programmatic access tools for cell type annotation. Covers 1,000+ cell types across hu

Paragraph — graph-based structural variant genotyper for short-read sequencing data from Illumina. Genotypes known deletions, insertions, duplications, and inversions from BAM/CRAM files using local g

ParSNP — rapid core-genome alignment and SNP detection for closely related microbial genomes (bacteria, archaea). Part of the HARVEST suite alongside HarvestTools and Gingr. Aligns hundreds of whole-g

pathfindR is an R package for active-subnetwork-oriented pathway enrichment analysis. It maps a gene list (typically a differential expression result with fold-changes and p-values) onto a protein-pro

PCGR (Personal Cancer Genome Reporter) — Python/R tool for automated annotation and clinical interpretation of somatic mutations and copy number aberrations in individual tumor genomes. Accepts somati

PDBe tools and Molstar — EMBL-EBI Protein Data Bank in Europe REST API combined with the Molstar 3D macromolecular structure viewer for retrieving, validating, and visualizing protein, nucleic acid, a

Pegasus — scalable single-cell RNA-seq analysis toolkit for millions of cells. Command-line tool and Python package for preprocessing, batch correction, clustering, differential expression, visualizat

MalariaGEN Pf3k/Pv4 pipelines — cloud-native Python API for accessing and analysing Plasmodium falciparum (Pf7/Pf8, 33K+ genomes) and Plasmodium vivax (Pv4, 1,895 genomes) population genomics data. Pr

pGlyco3 is an intact N- and O-glycopeptide search engine from pFind Studio. It uses a glycan-first search strategy with Y-ion evidence, supports monosaccharide modifications, provides glycan and pepti

PharmGKB — Pharmacogenomics Knowledge Base for curated gene-drug relationships, clinical pharmacogenomics annotations, drug pathway diagrams, and VIP gene summaries. Query the PharmGKB REST API for va

phASER (Phase and Allele Specific Expression from RNA) is a tool for phasing variants and quantifying allele-specific expression (ASE) from RNA-seq data. Use this skill for haplotype phasing with RNA-

Philosopher — fast, scalable Go toolkit for shotgun proteomics data analysis. Provides database downloading, peptide validation (PeptideProphet), protein inference (ProteinProphet), PTM localization (

Plotly — interactive graphing library for Python producing publication-quality figures as HTML, PNG, SVG, and PDF. Provides plotly.express for concise high-level charts (scatter, bar, line, heatmap, v

PopART (Population Analysis with Reticulate Trees) — Java-based application for constructing and visualizing haplotype networks from DNA sequence alignments. Supports TCS, Median-Joining, Minimum Span

Pore-C tools — Oxford Nanopore Technologies Python toolkit for processing Pore-C long-read chromatin conformation data. Converts raw nanopore reads into multi-way contact maps, supporting restriction-

Poseidon — a framework for organizing, sharing, and managing archaeogenetic genotype datasets. Standardized package format (POSEIDON.yml, .janno metadata, .ssf sequencing source files, .bib bibliograp

ProDy — Python library for protein dynamics analysis and structural bioinformatics. Provides elastic network models (GNM, ANM), principal component analysis (PCA) of structural ensembles and MD trajec

ProteinBERT — universal deep-learning model for protein sequences and function. Generate per-residue and global protein embeddings using a BERT-style transformer pretrained on 106 million UniRef90 seq

Proteome Discoverer — Thermo Fisher Scientific's integrated proteomics software platform for mass spectrometry data analysis. Provides SEQUEST HT and Mascot database searching, Percolator PSM validati

Use when working with ProtTrans — a collection of protein language models (ProtT5, ProtBert, ProtAlbert, ProtXLNet, ProtElectra) — for generating protein sequence embeddings, secondary structure predi

Use when working with pVACtools — pVACseq, pVACfuse, pVACbind, pVACvector — the Griffith Lab suite for neoantigen prediction and personalized cancer immunotherapy vaccine design. Predicts neoantigens

Pychopper — Nanopore direct cDNA read preprocessing tool that identifies, orients, and trims full-length reads using primer detection (pHMM or alignment). Rescues fused reads by dynamic programming, e

pygenometracks -- Python program and library for plotting publication-quality genome browser tracks. Generates highly customizable visualizations of bigwig, BED, GTF, bedgraph, Hi-C matrices, links/ar

PyMOL — molecular visualization system for rendering publication-quality 3D images of protein structures, nucleic acids, small molecules, electron density maps, and volumetric data. Provides interacti

pySCENIC — Python implementation of SCENIC for single-cell gene regulatory network inference and regulon analysis. Implements a three-step pipeline: GRN inference via GRNBoost2 or GENIE3, cis-regulato

PySTAC — pure-Python library for reading, writing, validating, and building SpatioTemporal Asset Catalogs (STAC) for geospatial data. Provides the core object model (Catalog, Collection, Item, Asset)

QIIME 2 — open-source microbiome bioinformatics platform for amplicon and marker-gene analysis. Plugin-based architecture with semantic type system enforcing data compatibility between analysis steps.

Use when querying, downloading, or analysing QTL data from the QTLbase database — a comprehensive multi-tissue, multi-omics QTL repository covering eQTL, sQTL, and pQTL studies across human and model

QuASAR (Quantitative Allele-Specific Analysis of Reads) — R package for detecting allele-specific expression (ASE) and allelic imbalance from RNA-seq data. Uses a beta-binomial model to test for ASE a

QuPath — open-source platform for whole slide image analysis and digital pathology. Provides interactive tools for tissue detection via thresholding, cell detection and positive cell classification (H

RawTools — open-source C# toolkit for parsing and quality control of Thermo Orbitrap RAW mass spectrometry files from DDA experiments. Extracts scan metadata, generates QC metrics for instrument monit

Rcorrector — kmer-based error correction for RNA-seq reads. Corrects Illumina sequencing errors in FASTQ data using Jellyfish2 bloom filters and adaptive kmer frequency thresholds. Handles non-uniform

RDKit — open-source cheminformatics toolkit written in C++ with Python bindings for molecular manipulation, descriptor calculation, fingerprinting, substructure searching, chemical reaction handling,

Reactome graph database — EMBL-EBI curated biological pathway knowledgebase with Neo4j graph backend and REST API. Supports pathway enrichment analysis, over-representation testing, graph topology tra

Use when working with ReactomePA — an R/Bioconductor package for Reactome Pathway Analysis. Performs over-representation analysis (ORA) and gene set enrichment analysis (GSEA) against the Reactome pat

REVEL (Rare Exome Variant Ensemble Learner) -- ensemble method for predicting the pathogenicity of rare missense variants in the human genome. Combines scores from 13 individual tools (SIFT, PolyPhen-

PacBio Revio tools — suite of command-line utilities for processing HiFi long reads generated by the PacBio Revio system. Covers CCS (circular consensus sequencing) generation with pbccs/ccs, demultip

Rfam — comprehensive database of non-coding RNA families and covariance models for RNA homology search. Annotate ncRNA sequences using Infernal's cmscan against the Rfam CM library, covering rRNA, tRN

RFdiffusion -- deep learning framework for protein structure generation via denoising diffusion on SE(3) protein backbone frames. Designs novel protein backbones including unconditional monomer genera

Use when reading or writing HDF5 files in R using the rhdf5 Bioconductor package. Covers h5read, h5write, h5createFile, h5createGroup, h5ls, h5closeAll, and chunked/compressed dataset creation. Trigge

Use when generating RNA sequence embeddings, predicting RNA secondary structure, or fine-tuning a foundation model on non-coding RNA tasks with RNA-FM. Covers installation, embedding extraction, fine-

Use when working with nf-core/rnafusion — a Nextflow pipeline for RNA fusion gene detection and quantification. Detects fusion transcripts from RNA-seq data using up to six callers (STAR-Fusion, Arrib

RNA-SeQC — fast C++ tool for RNA-seq quality control and gene-level quantification for large cohorts. Computes 70+ QC metrics including alignment rates, rRNA contamination, GC bias, 3'/5' coverage bia

RnBeads — comprehensive R/Bioconductor package for DNA methylation analysis. Supports Illumina Infinium arrays (450K, EPIC/850K), WGBS, RRBS, and other bisulfite sequencing platforms. Key capabilities

Roadmap Epigenomics — NIH Roadmap Epigenomics Mapping Consortium reference epigenomes spanning 111 primary human tissues and cell types. Provides ChIP-seq histone mark tracks (H3K4me1, H3K4me3, H3K27m

RStan — R interface to Stan for full Bayesian inference via MCMC (NUTS/HMC), approximate inference via ADVI, and penalized MLE via L-BFGS. Compile Stan programs in-process with stan() or stan_model(),