Browse Tools

Use when working with org.Mm.eg.db, mouse genome annotation, Mus musculus gene annotation in R, or Bioconductor AnnotationDbi lookups for mouse. The org.Mm.eg.db package provides genome-wide annotatio

Computational paleontology skill for non-DNA analysis of fossil data. Covers geometric morphometrics (landmark-based shape analysis with geomorph), diversity dynamics (extinction and origination rates

Use when working with pathview, the R/Bioconductor package for KEGG pathway-based data integration and visualization. Covers overlaying gene expression data (fold changes, p-values, counts) onto KEGG

PHASTER (PHAge Search Tool Enhanced Release) is a web server and REST API for rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Accepts NCBI accession nu

Phytozome utilities — search, browse, and download plant genome assemblies, gene annotations, protein sequences, and comparative genomics data from the JGI Phytozome plant genomics portal. Supports qu

PlasmoDB is the VEuPathDB genomic resource for Plasmodium and Apicomplexa parasites (Toxoplasma, Cryptosporidium, Babesia, Eimeria, and others). Query gene annotations, expression data, ortholog group

PlasmoDB — the Plasmodium genome resource and functional genomics database for malaria parasites. Part of VEuPathDB, it provides genomic, transcriptomic, and proteomic data for Plasmodium species incl

Use when working with Rsubread, the Bioconductor R package for read alignment, exon junction discovery, feature counting, long-read mapping, annotation flattening, and alignment QC. Covers buildindex(

scverse — the community-maintained Python ecosystem for single-cell and spatial omics analysis. Coordinates AnnData (universal data structure), scanpy (scRNA-seq QC/clustering/DE), squidpy (spatial tr

Use when working with ShortRead, the Bioconductor package for FASTQ and FASTA quality control, chunked read iteration, random sampling, filtering, trimming, and QA reporting in R. Covers FastqStreamer

SignalP predicts signal peptides and their cleavage sites in protein sequences. Use when users ask about SignalP, signal peptide prediction, secreted protein identification, Sec/SPI, Sec/SPII, Tat/SPI

SILVA — comprehensive quality-checked database of aligned ribosomal RNA (rRNA) sequences for Bacteria, Archaea, and Eukaryota. Provides SSU (16S/18S) and LSU (23S/28S) rRNA reference databases for tax

table2asn is the NCBI command-line tool for converting FASTA sequences and feature tables into ASN.1 (.sqn) files for submission to GenBank, RefSeq, and related NCBI databases. Handles prokaryotic and

TAIR (The Arabidopsis Information Resource) — the primary genomic database for Arabidopsis thaliana, providing gene models, functional annotations, protein sequences, metabolic pathways (AraCyc), stoc

TargetScan predicts biological targets of miRNAs in vertebrates by searching 3'UTR sequences for conserved matches to the miRNA seed region (8mer, 7mer-m8, 7mer-A1, 6mer sites). Computes context++ sco

TMHMM predicts transmembrane helices in protein sequences using a hidden Markov model. Use when users ask for transmembrane topology prediction, TM helix counting, inside/outside orientation assignmen

Use when working with topGO, the Bioconductor package for Gene Ontology enrichment analysis that accounts for the GO graph topology. Covers `topGOdata` object construction, `annFUN.org`, `annFUN.gene2

ToxoDB — integrated genomic and functional database for Toxoplasma gondii and related apicomplexan parasites within the VEuPathDB ecosystem. Provides gene search, BLAST, genome browser (GBrowse/JBrows

TriTrypDB is a VEuPathDB genomics platform for kinetoplastid parasites including Trypanosoma and Leishmania species. Use this skill for gene discovery, functional annotation lookup, orthology queries,

TriTrypDB — integrated functional genomics resource for kinetoplastid parasites (Trypanosoma, Leishmania, and related species). Part of the VEuPathDB Bioinformatics Resource Center, hosting 83+ annota

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

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

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

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

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

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

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

adehabitatHR (CRAN) home-range estimation for animal telemetry and relocation data in R. Routes users to Minimum Convex Polygon (mcp), kernel utilization distributions (kernelUD), Brownian bridge home

Use when working with biomaRt, BioMart queries in R, Ensembl annotation retrieval, cross-dataset identifier mapping, or annotation lookups through Bioconductor. biomaRt connects R to BioMart services

CDO (Climate Data Operators) is a collection of command-line operators for manipulating and analyzing Climate and Forecast (CF) data. Primary use cases include data processing, statistical analysis, a

CERVUS is a software package for parentage analysis and individual identification using codominant genetic markers (microsatellites, SNPs). Applies maximum-likelihood LOD scores and simulation-based c

ENCODE tools provide access to the Encyclopedia of DNA Elements data, including genomic functional elements, ChIP-seq, RNA-seq, and ATAC-seq data. Facilitates data retrieval, query, and analysis for e

Enrichr — web-based gene set enrichment analysis platform providing instant over-representation analysis against ~300 gene set libraries containing ~400,000 annotated gene sets. Implements Fisher's ex

Expression Atlas is the EMBL-EBI database and programmatic toolkit for querying baseline and differential gene expression across thousands of experiments in 50+ species. Use this skill to search exper

FactoMineR — R package for multivariate exploratory data analysis providing principal component analysis (PCA), correspondence analysis (CA), multiple correspondence analysis (MCA), multiple factor an

FlowJo v10 skill for flow-cytometry and mass-cytometry analysis workflows. Use when users need compensation setup, gating hierarchy design, batch processing, statistics table export, plugin-assisted a

Forensic genetics — probabilistic genotyping, STR mixture interpretation, kinship and paternity analysis, population allele frequency databases, and NGS-based forensic sequencing. Covers R packages: f

IRanges — core Bioconductor infrastructure for integer range and interval data manipulation in R. Create, manipulate, and query IRanges and GRanges objects for genomic interval arithmetic. Use for fin

LitVar — biomedical literature mining for genetic variants. Search PubMed and PMC full-text articles for mentions of SNPs, indels, and other genetic variants by rsID, gene name, or HGVS notation. Retr

The Matrix package for R provides a rich hierarchy of S4 classes for dense and sparse matrices. It enables efficient numerical linear algebra operations and is a foundational component of the R ecosys

NEB Tools is a suite of free online tools from New England Biolabs (NEB) for primer design, restriction enzyme selection, cloning strategy planning, and molecular biology workflow design. Key tools in

OpenWetWare is an open wiki platform for sharing biological research protocols, lab notebooks, standard operating procedures (SOPs), and experimental methods. Use to discover and retrieve community-cu

PacBio (Pacific Biosciences) is a company that develops and manufactures systems for gene sequencing. This skill provides tools to work with PacBio data.

Use when working with PharmVar (Pharmacogene Variation Consortium) to access curated pharmacogenomics variant data for CYP2D6, CYP2C19, CYP2C9, CYP3A5, DPYD, SLCO1B1, and other clinically actionable p

Raven Pro and Raven Lite bioacoustics software from the Cornell Lab of Ornithology for visualizing, measuring, and annotating audio recordings. Produces selection tables (tab-delimited .txt) with acou

Use when working with Rsamtools, the Bioconductor R package for indexed BAM, BCF, FASTA, and tabix-backed genomic files. Covers BamFile, ScanBamParam, filterBam, sortBam, indexBam, pileup, TabixFile,

This skill provides tools for working with data from the Trans-Omics for Precision Medicine (TOPMed) program. It includes capabilities for quality control, analysis, and visualization of large-scale g

Tools for interacting with the UNITE database for fungal ITS sequence data. Provides functionality for searching, downloading, and formatting UNITE reference datasets. Useful for metabarcoding and tax

Use when working with Bioconductor VariantAnnotation, VCF import in R, ScanVcfParam field or range subsetting, locateVariants(), predictCoding(), filterVcf(), or coding consequence workflows that comb

BioStudies and BioSamples are EMBL-EBI databases for storing and retrieving biological study metadata and sample provenance. BioSamples holds structured metadata for biological samples (accessions SAM