Browse Tools

tRNAscan-SE — genome-wide tRNA gene prediction tool that uses covariance models via Infernal to identify, score, and classify transfer RNA genes in eukaryotic, bacterial, archaeal, and mitochondrial s

Use when working with Bioconductor TxDb annotation packages, especially TxDb.Hsapiens.UCSC.hg38.knownGene, GenomicFeatures transcript models, UCSC knownGene annotations, gene and transcript coordinate

Use when working with UCell, an R/Bioconductor package for gene-set enrichment scoring in single-cell RNA-seq data using the AUCell rank-based method. Computes per-cell UCell scores for custom gene si

Use when working with UINMF in `rliger` for mosaic single-cell integration with shared and unshared features. UINMF extends LIGER's iNMF workflow to keep modality-specific genes, intergenic accessibil

UMAP (Uniform Manifold Approximation and Projection) — nonlinear dimensionality reduction for visualization and general-purpose embedding. Constructs fuzzy simplicial complex from high-dimensional dat

UpSetR is an R package for visualizing intersections of multiple sets using UpSet plots — a scalable alternative to Venn diagrams for 3+ sets. Use when you need to compare membership across gene lists

Use uwot for R-native UMAP and related manifold learning methods (`umap`, `umap2`, `tumap`, `lvish`, and `umap_transform`) on dense, sparse, and distance inputs. Route this skill when users ask for no

Use when working with VADR, the NCBI Viral Annotation DefineR suite for validating, classifying, and annotating viral genome sequences against VADR model libraries. Covers `v-scan.pl` for library-awar

Use when working with varbvs, the R package for large-scale Bayesian variable selection in genome-wide association studies (GWAS). Covers fitting variational Bayes models for continuous and binary phe

Use when working with the R/Bioconductor package variancePartition for quantifying the contribution of biological and technical factors to gene expression variability, fitting linear mixed models to R

VARITY -- machine-learning variant effect predictor for missense variants. Predicts pathogenicity of single amino acid substitutions using gradient boosting trained on ClinVar. Provides two models: VA

Use when working with VAST-TOOLS for alternative splicing analysis in RNA-seq data. Routes to references and scripts for VASTDB setup, splicing event quantification (PSI/PIR), differential splicing wi

VectorBase — bioinformatics resource for invertebrate vector genomics providing gene search, BLAST, genome browsing (JBrowse), population biology mapping (MapVEu), and REST API access for arthropod ve

velocyto.R skill for RNA velocity analysis in single-cell RNA-seq data. Use when users ask about velocyto.R, RNA velocity in R, deterministic velocity models, or working with .loom files containing sp

Use when working with VILOCA, the viral haplotype reconstruction and mutation calling tool for short-read and long-read sequencing data. Covers the `viloca` CLI, `run` and `snv` subcommands, quality-s

Use when working with viral-ngs, Broad Institute viral genomics tooling, viral sequencing pipelines, pathogen read depletion, metagenomic classification, viral assembly, or intrahost/interhost variant

VISION (Viewpoint Informed Sequencing Analysis of Networks) is an R package for interpreting single-cell RNA-seq data by linking gene expression signatures to cell metadata through an interactive web

Vitessce — interactive web-based visualization tool for exploration of multimodal and spatially resolved single-cell data. Use for configuring Jupyter widget layouts with VitessceConfig, loading OME-T

Use this skill for wallace workflows in R when you need a Shiny-based platform for reproducible species niche and distribution modeling, including occurrence-data retrieval, WorldClim environmental la

WeatherBench 2 is a benchmarking framework for next-generation data-driven global weather models. It provides tools for accessing re-forecast and observational data, computing performance metrics (RMS

xcms preprocesses LC-MS and GC-MS data in Bioconductor workflows. Use it for peak detection, retention-time alignment, feature grouping, and gap-filling when you need reproducible feature-by-sample in

ZFIN (Zebrafish Information Network) — the model organism database for Danio rerio (zebrafish). Provides curated gene records, expression data (in situ hybridization, antibody staining), mutant and tr

ZINB-WaVE (Zero-Inflated Negative Binomial Wave) for dimensionality reduction and normalization of single-cell RNA-seq data. Fits a zero-inflated negative binomial (ZINB) model to scRNA-seq count matr

Use when working with clinvar-tools — clinVar tools — NCBI utilities

EGA tools — EMBL-EBI European Genome-phenome Archive client and submission utilities. Covers encrypted download (pyEGA3), file encryption (EGA Cryptor), metadata schema validation, submission API inte

generate-cwl-from-nextflow — cross-compile Nextflow DSL2 process and workflow definitions into CWL v1.2 CommandLineTool and Workflow YAML documents for portable execution on CWL-compatible platforms (

GSEA — Gene Set Enrichment Analysis determines whether a priori defined gene sets show statistically significant, concordant differences between two biological states. Computes enrichment scores via a

H3 hexagonal hierarchical geospatial indexing for mapping latitude/longitude points and polygons to stable multi-resolution cells, running neighborhood traversal (grid disk/ring/distance), compacting

INLA (Integrated Nested Laplace Approximations) — R package for fast approximate Bayesian inference on latent Gaussian models. Provides deterministic approximations to posterior marginals as an altern

JACKS — Joint Analysis of CRISPR/Cas9 Knock-out Screens. Bayesian method for jointly estimating gene essentiality and gRNA efficacy across multiple CRISPR knockout screens. Shares information across c

Limnology (freshwater science) — computational toolkit for freshwater ecosystem analysis including lake thermal stratification (rLakeAnalyzer), lake metabolism estimation (LakeMetabolizer), eDNA metab

MPRADesignTools — R package for designing Massively Parallel Reporter Assay (MPRA) experiments. Provides oligo library design, sample size estimation, barcode generation, sequence tiling, and statisti

Use when working with OBO Foundry ontologies or the OBO tooling ecosystem: pronto (Python OBO/OWL parser), ROBOT (Java CLI for ontology operations), oaklib/OAK (Ontology Access Kit), or fastobo. Cover

Orphanet — global reference portal for rare diseases and orphan drugs. Provides ORPHA identifiers (ORPHA codes), the Orphanet Rare Disease Ontology (ORDO), gene-disease associations, clinical trial li

p.adjust — Multiple testing p-value correction in base R (stats package). Adjusts a vector of p-values using one of seven methods: Bonferroni, Holm (1979), Hochberg (1988), Hommel (1988), Benjamini-Ho

Wellcome Sanger Institute tools and resources — access COSMIC somatic mutation data, run Cancer Genome Project (CGP) WGS somatic variant calling pipelines (CaVEMan SNVs, Pindel indels, BRASS SVs, ASCA

SGD (Saccharomyces Genome Database) — the authoritative curated resource for Saccharomyces cerevisiae genome biology. Provides a REST API for querying genes, ORFs, phenotypes, GO annotations, genetic

Use this skill for systems biology model simulation with Tellurium when users ask to run Antimony or SBML models, generate time-course simulations, switch between deterministic and stochastic integrat

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IQ-TREE — efficient phylogenomic software for maximum likelihood tree inference. Integrates ModelFinder for automatic model selection (10-100x faster than jModelTest/ProtTest), ultrafast bootstrap (UF

Pierian Dx (now Velsera) Clinical Genomics Workspace (CGW) — comprehensive clinical interpretation and analysis platform for NGS data. Supports variant annotation, clinical significance assessment, re

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a fast, accurate gene prediction tool for prokaryotic genomes and metagenomes. Predicts protein-coding genes in bacterial and archae

AlphaFold Database — public repository of 200M+ AI-predicted protein structures maintained by DeepMind and EMBL-EBI. Access predictions by UniProt accession via REST API at alphafold.ebi.ac.uk. Downlo

HL7 FHIR Genomics — clinical genomic data exchange using FHIR R4/R5 profiles. Represent variants, haplotypes, copy-number alterations, and pharmacogenomics findings as interoperable FHIR resources (Mo

MetaPhlAn 4 + StrainPhlAn 4 — marker-gene-based metagenomic profiling and strain-level phylogenetics. MetaPhlAn profiles microbial communities at species level from shotgun metagenomes using ~5.1M uni

Use when working with NetworkX, graph analysis in Python, biological network analysis, protein-protein interaction networks, gene regulatory networks, metabolic networks, pathway analysis, network top

Use this skill when working with Movebank's animal-tracking platform, Movebank REST API, attribute dictionary, and official integration examples. Covers study discovery, authenticated and public data