Browse Tools

GeneAbacus — fast Go-based tool for counting and profiling sequencing reads within genes, chromosomes, or constructs from SAM/BAM files. Supports mRNA-seq, Ribo-seq, ChIP-seq, CLIP-seq, Structure-seq,

Use when working with GeneiASE — allele-specific expression (ASE) detection from RNA-seq data using phased heterozygous SNPs. Detects gene-level allelic imbalance by counting reference and alternative

GeneMark — gene prediction and genome annotation suite for prokaryotic and eukaryotic organisms. Identifies protein-coding genes in genomic DNA using Hidden Markov Models and self-training algorithms.

Use when working with the GENESIS R/Bioconductor package for statistical genetics, GWAS mixed models, population structure analysis, or kinship estimation. GENESIS provides PC-AiR for population struc

GenomePeek is a hosted marker-gene screen for rapid taxonomic inspection of prokaryotic genome and metagenome sequence files. It extracts reads matching conserved marker genes, assembles them, and cla

GenomeScope — reference-free genome profiling from k-mer count histograms. Estimates genome size, heterozygosity, and repeat content using a negative binomial mixture model. Supports diploid (GenomeSc

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 genomicfeatures — genomicFeatures — Bioconductor

GenomicSEM — R package for structural equation modeling (SEM) on genome-wide association study (GWAS) summary statistics. Enables fitting SEM models without individual-level SNP data, conducting multi

Use when working with GenVisR, the R/Bioconductor package for genomic cohort visualization. Supports cohort oncoprints with `Waterfall()`, protein-domain mutation maps with `Lolliplot()`, copy-number

Use when working with GEOquery, the Bioconductor R package for downloading, searching, and parsing NCBI Gene Expression Omnibus records into Bioconductor-friendly objects. Covers `getGEO()` for GSE/GS

ggalluvial — R package extending ggplot2 for alluvial diagrams (Sankey-style flow diagrams) that visualize categorical data flows, longitudinal transitions, and multi-variable category distributions.

Use when working with ggforce, the R package that extends ggplot2 with advanced geoms and statistical transformations for scientific visualization. Covers geom_mark_ellipse, geom_mark_hull, geom_mark_

Use when working with the R package ggpubr for publication-ready ggplot2-based visualizations in biomedical and life sciences contexts. ggpubr provides ggboxplot, ggviolin, ggbarplot, ggscatter, gghis

ggraph — R package extending ggplot2 for network and graph visualization. Provides a grammar-of-graphics approach to drawing nodes, edges, and layouts for arbitrary graph objects (igraph, tidygraph).

Fit Gamma-Poisson (negative binomial) generalized linear models for single-cell and spatial RNA-seq data. Use this skill for differential expression analysis, overdispersion estimation, pseudobulk agg

gnomAD Python Methods — The official Broad Institute Python library (`gnomad` on PyPI) for analyzing Genome Aggregation Database data with Hail. Use when users need to programmatically load gnomAD pub

gnomAD browser — Broad Institute web application and GraphQL API for exploring the Genome Aggregation Database (gnomAD). Use when users need to look up variant allele frequencies in population cohorts

gnomAD toolbox — Python utilities for querying gnomAD variant databases and population genetics data from the Broad Institute. Look up variant allele frequencies, population-stratified frequencies (af

GNPS/FBMN routing skill for metabolomics and lipidomics molecular networking via the Global Natural Products Social (GNPS) platform and Feature-Based Molecular Networking (FBMN) workflow. Use this ski

Use when working with GONE — Genomic Oscillations in Ne — a software tool for estimating historical effective population size (Ne) from genomic data using linkage disequilibrium (LD) patterns. Support

Gramene — comparative plant genomics database covering 100+ plant genomes including rice, maize, wheat, sorghum, and Arabidopsis. Provides gene search, cross-species ortholog and paralog mapping via g

Use when working with graph-tool for graph analysis, network science, community detection, stochastic block model (SBM) inference, or graph visualization in Python. graph-tool provides a fast C++/Open

Use when working with Graphein to build biomolecular and interaction graphs for geometric deep learning or network analysis. Covers protein structure graphs from PDB/AlphaFold, small-molecule graphs f

Use when working with GraphST for spatial transcriptomics analysis, including spatial domain clustering, multi-sample integration, and scRNA-to-spatial deconvolution. Trigger on "GraphST", "spatial tr

GSMR (Genome-wide Summary-data-based Mendelian Randomization) tests for putative causal relationships between complex traits using GWAS summary data only. Uses all GWAS-significant independent SNPs as

Use when working with GSVA (Gene Set Variation Analysis) for sample-wise gene set enrichment scoring from RNA-seq or microarray expression data. GSVA computes continuous enrichment scores per sample u

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

gwasglue — R package that connects IEU Open GWAS summary data to downstream statistical genetics analysis tools. Bridges GWAS summary statistics to Mendelian randomization (TwoSampleMR), colocalisatio

GWASLab is a Python toolkit for handling GWAS summary statistics (sumstats) with object-oriented workflows for loading, QC, harmonization, format conversion, and visualization. Use this skill when use

Use when working with GWASTools — a Bioconductor R package for quality control, management, and analysis of Genome-Wide Association Studies (GWAS). Covers reading GDS or netCDF genotype data with GdsG

gwasvcf — R package for reading, writing, and querying GWAS summary statistics stored in VCF format (GWAS-VCF specification). Provides fast variant extraction by chromosome/position, rsID, or p-value

HAPPI-GWAS (Holistic Analysis with Pre- and Post-Integration GWAS) routing skill for genome-wide association studies in food science, agriculture, and aquaculture. Use this skill when users mention HA

HDBSCAN for density-based clustering with variable-density groups and explicit noise labeling. Use this skill for `hdbscan.HDBSCAN`, cluster stability analysis, soft membership probabilities, GLOSH ou

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

Hecatomb is a viral metagenomics framework for short reads and long reads that wraps a Snakemake pipeline for preprocessing, iterative viral annotation, optional assembly, host-read removal, and downs

Helixer is a deep learning tool for eukaryotic gene prediction and annotation using cross-species LSTM models. Use it to predict gene structures (UTRs, exons, introns, intergenic regions) from raw gen

Use when estimating SNP heritability, local heritability, or genetic architecture from GWAS summary statistics. Covers per-locus heritability partitioning, total heritability estimation, LD matrix com

Use this skill for hicstuff, the Python CLI/library for Hi-C contact-map generation and manipulation. Covers end-to-end `hicstuff pipeline` execution, command-level workflows (`digest`, `filter`, `vie

HiCUP (Hi-C User Pipeline) is a modular pipeline for mapping and performing quality control on Hi-C sequencing data. Processes paired-end FASTQ reads through four stages: truncation at ligation juncti

HMDB tools routing skill for metabolomics and lipidomics compound annotation using the Human Metabolome Database. Use this skill when users mention HMDB, Human Metabolome Database, HMDB IDs, HMDB REST

CHORD (Classifier of Homologous Recombination Deficiency) — R package for predicting HRD status in tumors from somatic mutation patterns (SNVs, indels, structural variants). Uses random forest classif

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 iBioSim — a computer-aided design (CAD) tool for modeling, analysis, and synthesis of genetic regulatory networks (GRNs) and synthetic biology circuits. Supports SBML (Systems Bi

Use when working with ICTV-VBEG resources for computational virus taxonomy, phage assembly and annotation, phage genome download and reannotation, or mash-based phage community partitioning. Covers th

ieugwasr (IEU GWAS API in R) -- R package for querying the IEU GWAS database, accessing summary statistics from 47,000+ GWAS studies. Enables genome-wide association study data retrieval, effect size

IgFold — fast antibody structure prediction using language model embeddings. Predicts 3D structures of antibody variable domains (Fv) from amino acid sequence alone, without multiple sequence alignmen