Browse Tools

Minimac4 for genotype imputation from phased haplotype reference panels. Imputes missing genotypes using pre-phased target haplotypes and a reference panel in MVCF/M3VCF/VCF/BCF format. Use when perfo

MIRA (Multimodal models for Integrated Regulatory Analysis) for joint single-cell RNA-seq and ATAC-seq analysis. Provides probabilistic topic modeling, joint representation learning, pseudotime trajec

Mondo Disease Ontology — a comprehensive, cross-species disease ontology that harmonizes disease definitions from OMIM, Orphanet, Disease Ontology, NCBI, and other sources into a single unified hierar

mOTUs (marker gene-based Operational Taxonomic Units) is a computational tool for taxonomic profiling of microbial communities from metagenomic and metatranscriptomic shotgun sequencing data. Uses 10

Use when working with MR-PRESSO, Mendelian Randomization Pleiotropy RESidual Sum and Outlier, horizontal pleiotropy detection, outlier-corrected causal estimates, MR pleiotropy testing, distortion tes

Use when performing two-sample Mendelian randomization analysis with GWAS summary statistics using the mr.raps R package. mr.raps implements the Robust Adjusted Profile Score (RAPS) estimator to handl

PRSice-2 — fast polygenic risk score (PRS) calculator using clumping and thresholding (C+T). Performs LD clumping on GWAS summary statistics, applies p-value thresholds, computes PRS in target genotyp

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TwoSampleMR — R package for two-sample Mendelian randomization using GWAS summary statistics. Extracts genetic instruments from the IEU OpenGWAS database, harmonises exposure and outcome data, and app

WormBase is the model-organism knowledgebase for Caenorhabditis elegans and related nematodes. Use this skill when users need WormBase gene records, phenotype and interaction context, WormBase REST AP

Use when working with xTrimoGene or scFoundation-style single-cell foundation model inference for cell embeddings, gene embeddings, gene-batch embeddings, or xTrimoGene-based fine-tuning. Trigger this

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scales is the R package that powers ggplot2 value-to-aesthetic scaling, with functions for axis and legend labels, break generation, transformations, palettes, and range handling. Use this skill when

Use this skill for uv package-management and environment workflows across Python projects, scripts, tool execution, lockfile/sync flows, pip-compatible operations, and Python version installation/pinn

FHIR (Fast Healthcare Interoperability Resources) — HL7 standard for exchanging healthcare information electronically. Defines RESTful APIs and resource types (Patient, Observation, Condition, Diagnos

Jupyter notebooks and JupyterLab for interactive, reproducible, literate analysis workflows. Use this skill for creating, running, validating, and troubleshooting notebooks in local or CI pipelines; m

Use when working with nf-test for Nextflow pipeline testing, including test scaffolding, process/workflow/pipeline/function test generation, snapshot assertions, CI-safe snapshot updates, sharded exec

Use this skill when users need Nix package management, reproducible builds, flake-based workflows, dev shells, or hermetic CLI execution. Nix provides declarative dependency graphs, content-addressed

Ploomber is a Python pipeline framework for notebook and script based data workflows. Use this skill for pipeline.yaml (Spec API), directory entry-point, or factory entry-point workflows; for iterativ

PostGIS spatial extension for PostgreSQL. Use this skill for geometry/geography schema design, SRID management, loading WKT/WKB/GeoJSON, spatial joins, nearest-neighbor and distance queries, topology

Use this skill when users need pre-commit setup, hook execution, hook-stage routing, CI integration, configuration validation, hook revision pinning, or troubleshooting `.pre-commit-config.yaml` behav

protocols.io — cloud-based platform for creating, sharing, and executing reproducible lab protocols. Provides a REST API for protocol discovery, retrieval, and management. Supports lab automation inte

ScrumPy (Metabolic Modelling in Python) for structural and kinetic metabolic modeling using `.spy` model files, stoichiometric analysis, LP-based flux analysis, and elementary mode workflows. Use this

Use when configuring or troubleshooting Snakemake execution profiles for HPC and cloud environments. Covers global profiles (`--profile`), workflow profiles (`--workflow-profile`), profile config file

TileDB-SOMA (Stack Of Matrices, Annotated) routing skill for single-cell and spatial omics data management. Use this when users need SOMA Experiment/ Collection/DataFrame workflows, AnnData/Seurat int

VR-pipe/iRODS — Wellcome Sanger Institute tooling for managing genomics data in iRODS (Integrated Rule-Oriented Data System). Covers baton (batch iRODS metadata query client), npg_irods (Illumina/ONT

Use when users need Azure Batch for large-scale parallel or HPC workloads, including pool creation, autoscale policies, job/task submission, container tasks, and operational validation. Routes to offi

Use when working with BioModels, curated systems biology models, SBML model discovery, model metadata retrieval, model file manifests, COMBINE archive downloads, model identifier validation, or buildi

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Use this skill when building, running, or validating CompuCell3D (CC3D) multicellular simulations. Covers Cellular Potts Model workflows, Python-based steppables, headless execution with `python -m cc

Generate deep skill for GlyTouCan, a common repository for glycan structures.

Hail — scalable Python framework for genomic data analysis built on Apache Spark. Use when performing GWAS, variant quality control, sample QC, PCA, LD pruning, association testing, burden tests, or b

IMPUTE5 for genotype imputation from phased haplotypes and a reference panel. Performs fast, accurate imputation using the Li and Stephens hidden Markov model with the PBWT data structure for efficien

Monolix/NONMEM population PK/PD modeling skill for nonlinear mixed-effects workflows across GUI-first MonolixSuite and control-stream-driven NONMEM. Use when users need data formatting for ID/TIME/obs

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Use when working with pydicom to read, write, or manipulate DICOM medical imaging files in Python. Supports reading .dcm files with dcmread, accessing and modifying DICOM tags and pixel data, anonymiz

SRA Toolkit — NCBI command-line utilities for downloading, converting, and validating Sequence Read Archive (SRA) data. Provides prefetch for bulk download, fasterq-dump for high-speed SRA-to-FASTQ co

Use when working with SynBioHub, the open-source repository for synthetic biology designs using SBOL (Synthetic Biology Open Language). SynBioHub stores, retrieves, shares, and publishes genetic parts

Verde — climate-analysis-indices. A toolkit for processing, gridding, and modeling spatial climate/geospatial data in Python. Features include gridding (spline interpolation, trend estimation), proces

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Use this skill when deploying, operating, or troubleshooting JupyterHub for multi-user notebook access. Covers local installs, reverse-proxy setups, REST API automation, and Kubernetes deployments wit

This skill compiles a deep skill for funcotator, including finding GitHub repo/API docs, crawling documentation, extracting code examples, EDAM-annotating, adding citations (DOI/PMID), and scoring wit

Access and analyze climate model data using the Pangeo ecosystem.

This skill provides an interface to the Global Biodiversity Information Facility (GBIF) API through the R package 'rgbif'. It enables querying and retrieving biodiversity data, including occurrence re

Streamlines acquisition and use of environmental predictor datasets for Species Distribution Modeling (SDM).

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