Browse Tools

Find drop-in replacements or compatible alternatives for bioinformatics tools using EDAM ontology I/O compatibility matching. Searches 47,000+ tools with curated migration knowledge for 20+ common alt

Use when converting Illumina BCL (Binary Base Call) files to FASTQ format using BCL Convert, the successor to bcl2fastq. Supports all modern Illumina platforms including NovaSeq X, NovaSeq X Plus, Nov

Immcantation — integrated software suite for adaptive immune receptor repertoire (AIRR-seq) analysis of B-cell and T-cell receptors. Covers the full pipeline from raw FASTQ preprocessing (pRESTO) thro

MycoCLAP (Mycological Characterized and Listed Annotated Proteins) is a manually curated database of biochemically characterized fungal proteins from primary literature. Use when annotating fungal pro

BioRender — web-based platform for creating professional scientific figures, illustrations, and diagrams. Use for designing publication-quality figures for research papers, grants, posters, and presen

BUGS/WinBUGS — Bayesian inference Using Gibbs Sampling for complex hierarchical models via MCMC. Model specification in the BUGS language with stochastic (~) and deterministic (<-) nodes, 30+ distribu

CCP4 — Collaborative Computational Project Number 4 software suite for macromolecular X-ray crystallography. Provides programs for data processing (AIMLESS, POINTLESS), molecular replacement (Phaser),

cryoSPARC — cryo-EM single particle analysis platform for high-resolution 3D structure determination. Provides motion correction, CTF estimation, particle picking (blob, template, Topaz), 2D classific

Geneformer — transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-specific gene network analysis. Supports fine-tuning for cell type classification, gene

NCBI Genome Data Viewer (GDV) — interactive web-based genome browser for exploring RefSeq genome assemblies with gene, variant, and functional annotation tracks. Supports URL-based navigation to speci

Use when working with imagej — open-source image processing program with

Use when working with PubMedBERT — a BERT model pretrained from scratch on PubMed abstracts — for biomedical NLP tasks including named entity recognition, relation extraction, question answering, and

TCGA/GDC tools — NCI Genomic Data Commons Data Transfer Tool and API client for downloading cancer genomics data from TCGA, TARGET, CGCI, and related programs. Provides high-performance file downloads

Use when working with TreeMix for population genetics admixture graph inference, including input preparation from PLINK or VCF files, running maximum-likelihood tree fitting with migration events, and

Tools and workflows for accessing, querying, and analyzing data from the 1000 Genomes Project (1KGP) — the largest public catalog of human genetic variation with whole-genome sequences from 3,202 indi

10x Genomics — commercial platform for single-cell and spatial genomics assays including Chromium single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq, single-cell multiome (RNA+ATAC), Visium spatial

Use when querying ClinGen — the Clinical Genome Resource — for expert-curated gene-disease validity classifications, variant pathogenicity interpretations, dosage sensitivity assessments, and clinical

Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem

FlyBase is the primary model-organism knowledgebase for Drosophila melanogaster and related Drosophila species. Use this skill when users need FlyBase gene records, allele and phenotype data, transgen

Search publications for a bioinformatics tool — find peer-reviewed papers that use, cite, or benchmark a tool using PubMed E-utilities, CrossRef REST API, and OpenAlex scholarly graph. Aggregates cita

Radiation biology computational toolkit — Linear-Quadratic (LQ) model for cell survival, BED and EQD2 dose-equivalence conversions, clonogenic survival curve fitting, TCP/NTCP modelling, DVH analysis,

Infer bioinformatics file format from magic bytes, header patterns, and file extensions

Optogenetics skill for designing, analyzing, and interpreting light-based neural circuit manipulation experiments. Covers opsin selection (ChR2, halorhodopsin, Arch, C1V1, jRCaMP), viral vector strate

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DrugBank tools — comprehensive pharmaceutical database access for drug information, drug-drug interactions, pharmacokinetics, drug targets, and pharmacogenomics data via the DrugBank REST API and bulk

GROMACS — high-performance molecular dynamics simulation engine for biomolecular systems. Simulates Newtonian equations of motion for hundreds to millions of particles using leap-frog, velocity Verlet

nlme — Linear and Nonlinear Mixed-Effects Models in R. Fit hierarchical and repeated-measures data with lme() for linear models and nlme() for nonlinear models. Supports nested random effects, within-

Use when working with S4Vectors — core Bioconductor infrastructure

UK Biobank tools — access, convert, and analyse UK Biobank phenotypic and genetic data using ukbconv, gfetch, ukbtools (R), and the UK Biobank DNAnexus Research Analysis Platform. Covers field decodin

BeetleBase is the model organism database for Tribolium castaneum (red flour beetle), covering genome browsing, BLAST searches, gene model retrieval, GO annotation, RNAi phenotype data, and synteny an

Use when working with Bioconductor BiocGenerics, the R package that defines S4 generic functions shared across the Bioconductor ecosystem. Route users who need to understand how Bioconductor generics

Use when working with Bioconductor AnnotationDbi, the R package that provides a common interface for SQLite-backed annotation packages such as OrgDb, ChipDb, GO.db, and custom AnnotationDb derivatives

BLD-LDAK (SumHer) — LD-adjusted heritability and genetic architecture estimation from GWAS summary statistics. Implements BLD-LDAK, LDAK-Thin, and SumHer models for SNP heritability partitioning, enri

Use when working with BSgenome, Bioconductor whole-genome sequence packages, getBSgenome(), getSeq(), bsapply(), injectSNPs(), genome FASTA export, or masked BSgenome objects in R. BSgenome provides t

COSMIC (Catalogue Of Somatic Mutations In Cancer) is the authoritative curated database of somatic mutations driving human cancer, maintained by the Wellcome Sanger Institute. Use this skill for query

EMBL-EBI (European Bioinformatics Institute) — access bioinformatics databases and analysis services from EMBL-EBI including EBI Search for cross-database discovery, EMBL-EBI Tools Job Dispatcher for

Ensembl Vet Tools — bioinformatics resources for veterinary and livestock genomics using the Ensembl infrastructure. Covers genome browsing for FAO Priority Livestock Species (cattle, pig, chicken, sh

GenAlEx — Microsoft Excel add-in for population genetics analysis. Implements AMOVA, PCA, PCoA, FST, genetic distance, and assignment tests within Excel worksheets. Supports microsatellite, SNP, haplo

Use when working with GenomicAlignments, GAlignments, GAlignmentPairs, summarizeOverlaps(), summarizeJunctions(), coverage() on BAM files, splice junction counting, paired-end alignment import, or Bio

Use when working with Gviz, the Bioconductor R package for plotting genomic coordinates, annotations, signal tracks, read alignments, and sequence context in genome-browser-style figures. Covers core

HDF5Array — Bioconductor R package providing HDF5-backed DelayedArray objects for out-of-memory access to large genomics matrices. Core infrastructure for single-cell RNA-seq workflows. Key classes: H

Use when working with the i5k Workspace@NAL for insect and arthropod genome browsing, annotation, and analysis. Covers genome data access via JBrowse, Apollo-based manual annotation, data uploads (FAS

Use when working with JGI MycoCosm, the DOE Joint Genome Institute fungal genomics portal. Covers downloading fungal genome assemblies, gene annotations, and proteomes from the MycoCosm database; prog

LDAK — LD-adjusted kinship toolkit for SNP heritability estimation, genetic architecture analysis, and genomic prediction. Computes LDAK-Thin and LDAK-GCTA kinship matrices, estimates per-chromosome a

Use when performing differential gene expression analysis on RNA-seq count data using limma-voom. Covers the full workflow: count filtering with filterByExpr, TMM normalization via edgeR calcNormFacto

Long Ranger is 10x Genomics software for processing linked-read sequencing data from the Chromium Genome and Exome kits. Use this skill when users need to run `longranger wgs` for whole-genome phased

MASS — Modern Applied Statistics with S. R package providing negative binomial GLMs via glm.nb(), robust linear models via rlm() with Huber/bisquare/Hampel psi functions, linear and quadratic discrimi

MR-Egger is an R-based Mendelian randomization method that estimates causal effects from GWAS summary statistics while allowing directional pleiotropy via an unconstrained intercept term. Use when tes

NCBI/NIH tools — search, retrieve, and process biological data from NCBI databases (PubMed, GenBank, Gene, SRA, RefSeq, ClinVar, dbSNP, Taxonomy) using the NCBI E-utilities REST API and NCBI Datasets

Use when performing differential expression analysis on RNA-seq count data using NOISeq or NOISeqBIO. Covers the full workflow: data object creation with readData, quality control with dat and explo.p