Browse Tools

climlab is a flexible Python package for process-oriented climate modeling, enabling the creation of 1D radiative-convective and energy balance models (EBMs) to study Earth's climate system, greenhous

Use when working with Copernicus Climate Data Store programmatic retrieval via the CDS API Python client (`cdsapi`). Covers authentication with `.cdsapirc`, building valid dataset-specific request pay

Cryobiology computational tools for cryopreservation protocol design, cell survival modeling, and optimal cooling rate calculation. Implements Mazur's two-factor hypothesis (osmotic injury + intracell

Use when working with CytoML for cross-platform flow cytometry and mass cytometry workspace interchange between FlowJo, Cytobank, Diva, and the RGLab stack (`flowWorkspace`/`openCyto`). Covers importi

Use this skill for Dask-based parallel and distributed Python workflows, including delayed/task-graph execution, Dask Array/DataFrame tuning, scheduler selection (threads/processes/distributed), clust

dbGaP tools — NCBI/dbGaP controlled-access retrieval workflow for human genotype, phenotype, and sequence datasets. Covers the Authorized Access portal, PI and downloader roles, dbGaP File Selector, S

Use when working with DeepVirFinder for identifying viral contigs from metagenomic assemblies with the upstream `dvf.py` workflow. Covers FASTA input review, sequence-length cutoffs, model-bucket sele

Use when developing R packages with devtools, including load_all, document, test, check, build, install, release checks, and GitHub installation flows. Trigger for requests about R package development

dismo (R) for species distribution modeling (SDM) with presence-only and presence-background workflows. Use when users need Bioclim, Domain, Mahalanobis, MaxEnt integration, random background sampling

Use this skill for Distance R package workflows: line transect or point transect detection-function fitting with ds(), model comparison via AIC and summarize_ds_models(), goodness-of-fit checks with g

eofs is a Python package for empirical orthogonal function (EOF) analysis of spatial-temporal data in climate, meteorology, and oceanography. Use this skill when the user needs EOF decomposition, prin

ESMValTool (Earth System Model Evaluation Tool) is a community-developed diagnostics and evaluation software package for Earth system models, particularly for CMIP intercomparison. It streamlines the

eulerr — R package for drawing area-proportional Euler and Venn diagrams with circles or ellipses. Takes named numeric vectors, logical matrices, or data.frames describing set memberships or intersect

fancyimpute — Python library for multivariate imputation and matrix completion providing KNN imputation (weighted nearest neighbors), SoftImpute (iterative SVD soft-thresholding), IterativeSVD (low-ra

This skill provides tools for working with FinnGen data. NOTE: This is a placeholder due to tool access limitations.

fishflux is a tool for ...

flexsurv — Flexible Parametric Survival and Multi-State Models. R package for parametric time-to-event analysis with right-censored, left-censored, and left-truncated data. Core functions: flexsurvreg

Use when modeling neural power spectra with FOOOF/specparam (spectral parameterization) to separate aperiodic 1/f structure from periodic peaks. Routes EEG/MEG/LFP workflows for SpectralModel, Spectra

Use when working with formattable in R, formatted vectors, HTML table styling, formatter formulas, color tiles and bars, or reproducible table presentation in R Markdown, Shiny, and htmlwidgets. forma

formulaic — high-performance Python library for parsing Wilkinson-notation formulas and materialising model matrices from pandas DataFrames. Converts R-style formula strings (e.g. "y ~ x1 + x2 * x3")

Python client (pygbif) for the Global Biodiversity Information Facility (GBIF) API. Enables programmatic discovery and retrieval of species occurrence records, taxonomic name resolution, dataset metad

Use this skill for GDAL/OGR command-line and Python-adjacent geospatial workflows involving raster inspection, raster translation, reprojection, vector inspection, vector format conversion, and geomet

GenCast is Google DeepMind's diffusion-based machine learning model for probabilistic medium-range ensemble weather forecasting. It produces 15-day global ensemble forecasts at 0.25° resolution with 1

ggridges is an R package extending ggplot2 to create ridgeline plots (also called joy plots) for visualizing distributions of a continuous variable across multiple categories or groups. Use this skill

Use when users need GitHub Actions workflow authoring, CI/CD pipeline setup, workflow debugging, reusable workflows, matrix builds, artifact handling, or secure automation in repositories. Routes task

Use when working with GlyConnect, the ExPASy glycosylation knowledgebase for contextual glycoprotein evidence, glycan compositions, literature-backed glycosylation sites, and linked search workflows a

Use when working with glypy for glycan parsing, serialization, composition arithmetic, mass calculation, and glycan-structure operations in Python. Covers official glypy docs for GlycoCT and IUPAC IO

GNNExplainer explains predictions made by graph neural networks by learning sparse masks over subgraph structure and node features. Use for post-hoc GNN interpretability, identifying important edges a

GSW-Python is the Python implementation of the TEOS-10 Gibbs SeaWater toolbox for seawater thermodynamics and derived oceanographic diagnostics. Use this skill for practical salinity to absolute salin

The GTEx Pipeline is a standardized RNA-seq processing pipeline for the TOPMed project. It enables reproducible and harmonized analysis of gene expression, generating aligned reads, QC metrics, and bo

HydroMT (Hydro Model Tools) — open-source Python framework for automated building, updating, and analysis of spatial geoscientific models with a focus on water systems. Provides a model-agnostic inter

Use when working with the R package iNEXT for rarefaction and extrapolation of species diversity curves using Hill numbers. iNEXT supports sample-size-based and coverage-based interpolation/extrapolat

INTACT (INTegration of Aggregate GWAS and Colocalization to Trait-gene associations) is an R package that integrates TWAS (Transcriptome-Wide Association Study) evidence with probabilistic colocalizat

Use when working with iPHoP, the Integrated Phage Host Prediction command-line pipeline for predicting bacterial or archaeal host taxonomy from phage and archaeal virus genomes. Covers `iphop predict`

JBEI ICE (Inventory of Composable Elements) is an open-source biological parts registry for managing DNA constructs, plasmids, strains, and other biological materials via a REST API. Use ICE to search

Use when working with Koogu, the Python library for bioacoustics and animal sound detection and classification. Covers loading audio recordings, applying call detectors, training CNN-based species cla

Use when linting R code with r-lib/lintr for style, static analysis, and CI policy enforcement. Covers linting single files (`lint()`), project trees (`lint_dir()`), and packages (`lint_package()`), c

LION/web (Lipid Ontology Web) — ontology enrichment tool for lipidomics data. Translates lipidomics datasets into biological insights using target-list mode (Fisher's exact test) and ranking mode (Kol

lmerTest — R package extending lme4 to provide p-values for linear mixed effects models via Satterthwaite's and Kenward-Roger degrees of freedom approximations. Fits random-intercept and random-slope

lubridate is the tidyverse R package for parsing, rounding, shifting, and validating dates, date-times, and time spans. Use this skill when a user asks about `ymd()`, `ymd_hms()`, `parse_date_time()`,

Manim — Python library for programmatic mathematical animation. Renders geometric shapes, equations (LaTeX), graphs, number lines, and 3-D scenes to MP4/GIF. Two actively maintained forks: ManimGL (3b

Import, plot, and analyze bathymetric and topographic data in R. The `marmap` package provides helpers to query ETOPO bathymetry from NOAA, manipulate `bathy` grid objects, draw 2D and 3D seafloor map

mashr — Multivariate Adaptive Shrinkage in R for large-scale multiple testing and effect size estimation across conditions. Fits mixture-of-multivariate-normal priors to jointly shrink thousands of ef

MaxEnt (Maximum Entropy Modeling) for species distribution and ecological niche modeling from presence-only occurrence records and environmental predictors. Use this skill for SDM/ENM workflows, habit

MCMCglmm — Bayesian Multivariate Generalised Linear Mixed Models via MCMC in R. Fit complex hierarchical models with MCMCglmm() supporting 15+ response families (gaussian, poisson, categorical, ordina

mgcv — Mixed GAM Computation Vehicle with Automatic Smoothness Estimation. Fit generalized additive models (GAMs) with penalized regression splines via gam(), large-dataset GAMs with bam(), and genera