Browse Tools

Monarch Initiative tools — query disease-phenotype-gene associations, compute semantic similarity across species, and access biomedical ontologies (HPO, MONDO, GO, MP) via monarch-py Python client and

mrgsolve — R package for simulation from ODE-based PK/PD and systems pharmacology models with C++ model code, NONMEM-style event/data inputs, and high-throughput population simulation workflows. Use w

Use when working with NetMHCpan 4.1 for MHC class I peptide binding and ligand presentation prediction. NetMHCpan accepts peptide lists or FASTA proteins, scores candidate ligands against up to 20 all

Nextflow Tower / Seqera Platform CLI (`tw`) for launching and monitoring Nextflow pipelines, managing workspaces, credentials, compute environments, and runs from the command line. Use this skill for

NiMARE (Neuroimaging Meta-Analysis Research Environment) for coordinate- and image-based neuroimaging meta-analysis in Python. Use this skill when users need ALE or MKDA analyses, NiMARE Studyset/NIMA

Use when working with Nipype for neuroimaging workflow automation, pipeline construction, or wrapping FSL, FreeSurfer, SPM, AFNI, or ANTs interfaces. Nipype provides a uniform Python interface to hete

Use when working with nitime, neuroimaging time-series analysis, or neural signal processing in Python. This skill routes to canonical references and scripts for TimeSeries construction, spectral anal

A skill for visualizing shifts in marine animal distributions across North America using bottom trawl survey data. This skill guides users on how to use the OceanAdapt scripts, which rely on ArcGIS an

Open Targets Platform is an open-source drug target discovery platform from EMBL-EBI integrating genetic, genomic, and clinical evidence to identify and prioritise drug targets. Query target-disease a

Use when working with openCyto — the Bioconductor framework for automated, reproducible flow cytometry gating. Applies hierarchical gating strategies defined in a CSV template to GatingSet objects (fl

Opentrons Python Protocol API v2 — automate liquid handling on OT-2 and Opentrons Flex laboratory robots. Write Python protocols to control pipettes, labware (plates, tip racks, reservoirs), and modul

Use this skill for R package installation and dependency resolution with pak, including CRAN, Bioconductor, GitHub, git, local paths, and URL sources. Covers pkg_install workflows, package reference s

The R future package provides a simple and uniform API for evaluating R expressions asynchronously using various resources. Used when a user mentions "future", "parallel-future", "parallel processing

Parsl (Parallel Scripting Library) for building Python-native parallel and distributed workflows across local machines, HPC schedulers, and cloud resources. Use when tasks should be expressed with pyt

pcalg — R package for causal structure learning and causal inference using graphical models. Constraint-based algorithms (PC for no hidden variables, FCI/RFCI for latent confounders), score-based meth

Use when working with pgenlib — Python library for reading and writing

Use when working with PhyDyn, the BEAST2 package for phylodynamic inference with deterministic compartmental epidemic models defined as ordinary differential equations. Covers PopModelODE model specif

Use this skill for PhysiCell multicellular simulation workflows, including project selection with Makefile targets, OpenMP-ready build checks, XML settings validation, deterministic run-command genera

Use this skill when working with Pillow (PIL fork) for scientific image preprocessing, format conversion, resizing, metadata-aware export, and publication figure preparation in Python. Triggers includ

Use this skill for pkgdown workflows that build, customize, validate, and publish documentation websites for R packages. Covers `pkgdown::build_site()`, section-specific builders such as `build_refere

Microsoft Planetary Computer SDK and STAC workflow skill for signed geospatial asset access in Python. Use this when users ask about STAC item search, `pystac-client` integration, `planetary_computer.

Podman skill for building, running, validating, and troubleshooting Linux containers without a daemon using OCI-compatible workflows. Use when users ask about podman run/build/pod, rootless containers

Use when working with PRIME-Del, primedel, paired pegRNA deletion design, prime editing deletions, or short insertion-at-deletion workflows. PRIME-Del designs paired pegRNAs from a single FASTA target

A functional programming toolkit for R. Provides a complete and consistent set of tools for working with functions and vectors, designed to replace many for loops with code that is more succinct and e

Python implementation of the Mann-Kendall trend test and Sen's slope estimator. Used for detecting monotonic trends in climate data, hydrology, and environmental time-series. Includes support for seas

pyproj — Python interface to PROJ for cartographic projections and coordinate reference system (CRS) transformations. Converts coordinates between geographic (latitude/longitude), projected (UTM, Web

pySBOL3 — Python library for the Synthetic Biology Open Language (SBOL) 3 standard. Creates, reads, validates, and writes SBOL3 documents encoding biological designs as structured RDF data (N-Triples,

pytest is the Python testing framework for unit, integration, and regression tests with plain assert statements, fixture injection, parametrization, markers, and plugin-based extension. Use this skill

Use this skill for QGIS desktop, PyQGIS, and qgis_process command-line workflows in geospatial analysis. Covers vector overlays, buffering, reprojection, batch geoprocessing, model-friendly automation

Quarto CLI for reproducible scientific and technical publishing from markdown-first source files. Use this skill when users mention Quarto, .qmd files, literate programming, executable notebooks, para

Use when working with Quilt and quilt3 for scientific data package management on AWS. Covers package creation with Package.set() and Package.set_dir(), versioned manifests with Package.build() and Pac

Use this skill for R raster package workflows that create, crop, mask, reproject, summarize, and validate gridded spatial data with RasterLayer, RasterStack, and RasterBrick objects. Routes to documen

Rasterio — geospatial-gis-tools for reading and writing geospatial raster data. Provides seamless integration with NumPy, advanced raster processing (resampling, reprojection, windowed reading/writing

Ray is a distributed Python runtime for scaling compute-intensive workloads from a laptop to a cluster. Use Ray Core for task and actor parallelism, Ray Data for distributed ETL, Ray Train for distrib

ReefCloud is a tool for marine biology and oceanography, focused on coral reef analysis. It helps researchers analyze images of coral reefs to monitor their health and composition.

REINVENT4 — AI-driven de novo molecular design platform for drug discovery using reinforcement learning (RL) and generative models. Generate novel SMILES, decorate scaffolds (LibInvent), design linker

renv is the R project environment and dependency management toolkit for reproducible analysis. Use it to initialize isolated project libraries, capture dependency state in renv.lock, restore exact pac

Use when working with repo2docker or jupyter-repo2docker to reproducibly build and optionally run container images from source repositories using binder-compatible configuration files. Covers reposito

rgdal (R) bindings for GDAL and PROJ for legacy sp-class vector/raster IO, layer discovery, and CRS transformation workflows. Trigger this skill for readOGR/writeOGR, ogrListLayers, GDALinfo, and spTr

R Markdown (rmarkdown) is an R package for literate programming and reproducible reporting that combines prose, executable code chunks, and rendered artifacts into HTML, PDF, Word, slide decks, and mo

R client for the Ocean Biodiversity Information System (OBIS).

Ruff is a fast Python linter and formatter written in Rust. Use this skill when users ask to lint Python code, auto-fix violations, enforce style in CI, replace Flake8 or Black workflows, tune pyproje

Use when working with Sapiens — a BERT-based human antibody language model for antibody humanization, humanness scoring, and sequence design. Sapiens predicts humanizing mutations, scores residue-leve

scFates is a Python package for advanced pseudotime and bifurcation analysis of single-cell data. It provides scalable tree inference (ElPiGraph, SimplePPT), root selection, pseudotime calculation, an

Use when working with scikit-survival — the Python library for survival analysis built on top of scikit-learn. Supports Cox proportional hazards (CoxPH, CoxnetSurvivalAnalysis/LASSO), survival forests

SemMedDB is a repository of semantic predications (subject-predicate-object triples) extracted from PubMed/MEDLINE citations using the SemRep NLP system. It maps biomedical text to UMLS concepts and s

Use when working with sf (R), the Simple Features package for spatial vector data in data frames. Routes tasks for reading and writing GIS layers with GDAL, constructing geometries with st_as_sf, tran