Browse Tools

ClimaX — Vision Transformer foundation model for weather and climate science from Microsoft Research. Pretrained on CMIP6 via self-supervised learning, then fine-tuned for global forecasting (ERA5), r

Compare container images for bioinformatics tools across BioContainers (quay.io/biocontainers), DockerHub, and Galaxy Singularity depot. Returns available versions, image sizes, pull commands for Dock

CRISPRscan — sequence-based scoring algorithm for predicting CRISPR/Cas9 sgRNA on-target efficiency. Uses a linear regression model trained on zebrafish injection data to score 20-mer guide sequences

CWL (Common Workflow Language) — open standard for describing portable, reproducible computational workflows. Covers cwltool reference runner, CWL v1.2 spec, CommandLineTool and Workflow classes, Dock

DAGitty — graphical analysis of causal models using directed acyclic graphs (DAGs). Create DAGs with dagitty(), identify minimal adjustment sets for unbiased causal effect estimation (adjustmentSets),

Dendroscope — interactive viewer for large phylogenetic trees and rooted networks. Handles hundreds of thousands of taxa with smooth navigation. Supports Newick, Nexus, and phyloXML input; exports PNG

DrugBank tools — comprehensive pharmaceutical database access for drug information, drug-drug interactions, pharmacokinetics, drug targets, and pharmacogenomics data via the DrugBank REST API and bulk

Fiona is a geospatial data access library for Python, providing a simple, Pythonic API for reading and writing vector spatial data (e.g., Shapefile, GeoJSON, GPKG). Essential for spatial data ingestio

FourCastNet — NVIDIA's global data-driven weather forecasting model using Adaptive Fourier Neural Operators (AFNO) on a vision transformer backbone. Generates 0.25-degree resolution global forecasts i

glmmTMB — R package for fitting generalized linear mixed models (GLMMs) and extensions using Template Model Builder. Supports zero-inflation via ziformula, dispersion modeling via dispformula, and 15+

GROMACS — high-performance molecular dynamics simulation engine for biomolecular systems. Simulates Newtonian equations of motion for hundreds to millions of particles using leap-frog, velocity Verlet

HydroEval — Python evaluator for streamflow simulations using vectorized NumPy computation. Provides Nash-Sutcliffe Efficiency (NSE), Kling-Gupta Efficiency (KGE, KGE', KGEnp), RMSE, MARE, Percent Bia

Use when predicting MHC binding, T cell epitopes, B cell epitopes, or performing immunoinformatics analysis with IEDB Analysis Resource tools. Covers MHC-I and MHC-II binding prediction, BepiPred B-ce

Data cataloging utility for Earth System Model (ESM) data. Simplifies searching, discovering, and loading complex climate and weather datasets (e.g., CMIP6, CESM) into xarray Datasets. Supports JSON c

JM / JMbayes2 — Joint models for longitudinal and time-to-event data under the Bayesian framework. Fits shared-parameter joint models via jm() linking mixed-effects longitudinal submodels (lme, mixed_

Use when working with JupyterLab, the web-based interactive development environment for notebooks, code consoles, terminals, and text files. Covers installation, launching `jupyter lab`, workspace imp

kableExtra — R package extending knitr's kable() with advanced HTML and LaTeX/PDF table styling for R Markdown and Quarto documents. Provides Bootstrap themes, conditional row/cell formatting, column

Use when working with Kilosort — the GPU-accelerated spike sorting software for high-density extracellular electrophysiology recordings. Covers Kilosort4 (Python, PyTorch-based), probe/channel map con

lifelines — Python survival analysis library for time-to-event data. Fits Kaplan-Meier curves with KaplanMeierFitter(), Nelson-Aalen cumulative hazard with NelsonAalenFitter(), semiparametric Cox prop

Use when working with loftee — LOFTEE (Loss-Of-Function Transcript Effect

MDAnalysis — Python library for analyzing molecular dynamics trajectories and atomic coordinate data. Supports 40+ file formats (DCD, XTC, TRR, PDB, GRO, AMBER, LAMMPS). Provides RMSD, RMSF, hydrogen

MDTraj — Python library for reading, writing, and analyzing molecular dynamics trajectories. Supports 20+ formats (DCD, XTC, TRR, PDB, HDF5, NetCDF, etc.) with NumPy-native arrays. Provides RMSD, RMSF

mice — Multivariate Imputation by Chained Equations for handling missing data in R. Fully Conditional Specification (FCS) with 9+ built-in methods (pmm, norm, logreg, polyreg, polr, cart, rf, mean, ld

'Use when working with midas — miDAS — Multiple Imputation with Denoising

nbconvert converts Jupyter notebooks (.ipynb) into static formats including HTML, Markdown, LaTeX, PDF, WebPDF, slides, and executable scripts, and can optionally execute notebooks before export. Use

NCBI Datasets CLI — command-line tool for downloading genome, gene, virus, and taxonomy data directly from NCBI databases. Provides the `datasets` command for downloading and summarizing RefSeq/GenBan

nlme — Linear and Nonlinear Mixed-Effects Models in R. Fit hierarchical and repeated-measures data with lme() for linear models and nlme() for nonlinear models. Supports nested random effects, within-

OpenMRS is an open-source electronic medical record (EMR) and health information system platform for resource-constrained healthcare environments. Provides patient registration, clinical observations,

Pixi — fast, cross-platform package manager for conda and PyPI packages with project-level lockfiles and built-in task runner. Uses pixi.toml manifest for reproducible, multi-platform environments. Id

Poetry is the Python dependency management and packaging tool for creating reproducible projects with pyproject.toml and poetry.lock. Use this skill for dependency resolution, virtual environment isol

PyAEDT — Python library for automating Ansys Electronics Desktop (AEDT) electromagnetic, thermal, and circuit simulations. Provides unified API for HFSS (high-frequency EM), Icepak (thermal management

RNAcentral is the comprehensive non-coding RNA sequence database aggregating sequences from 40+ expert databases (miRBase, Rfam, lncRNAdb, Ensembl, HGNC, GENCODE, and more) under unified URS identifie

rstanarm — Bayesian Applied Regression Modeling via Stan. Fit Bayesian regression models using pre-compiled Stan programs with familiar R syntax: stan_glm() for generalized linear models, stan_glmer()

rstpm2 — R package for generalized survival models (GSMs), smooth accelerated failure time (AFT) models, and Markov multi-state models. Flexible parametric survival analysis via stpm2() with natural s

Use when working with S4Vectors — core Bioconductor infrastructure

Shapely — Python library for manipulation and analysis of planar geometric objects. Create and manipulate points, lines, polygons, and collections via Point(), LineString(), Polygon(), MultiPolygon().

PyTorch Geometric (PyG) — graph neural network library built on PyTorch for learning on graphs and irregular structures. Provides message-passing layers (GCN, GAT, GraphSAGE, GIN, Transformer), mini-b

twoBitToFa / faToTwoBit — UCSC Kent utilities for converting between the compact binary .2bit genome format and FASTA. twoBitToFa extracts sequences (full genome or specific regions) from a .2bit file

UK Biobank tools — access, convert, and analyse UK Biobank phenotypic and genetic data using ukbconv, gfetch, ukbtools (R), and the UK Biobank DNAnexus Research Analysis Platform. Covers field decodin

Wave — on-demand container provisioning service by Seqera Labs for building, augmenting, and caching container images dynamically. Supports Dockerfile-based builds, Conda/Mamba package-based image cre

Wflow — Deltares open-source distributed hydrological modeling framework written in Julia. Provides SBM, HBV, and sediment model configurations for catchment hydrology simulation. Uses TOML configurat

WhiteboxTools — advanced geospatial data analysis platform with 518 tools for GIS operations, hydrological analysis, terrain analysis, LiDAR processing, remote sensing, and geomorphometry. Supports ra

xCDAT (Xarray Climate Data Analysis Tools) — Python library for climate data analysis on structured grids. Extends xarray for CF-compliant spatial averaging, temporal climatologies, departures (anomal

3D-DNA — Hi-C-based genome scaffolding pipeline that produces chromosome-length assemblies from draft contigs and Hi-C contact maps. Performs iterative misjoin correction, scaffolding, polishing, chro

ABF (Approximate Bayes Factor) fine-mapping for GWAS loci. Compute per-variant posterior inclusion probabilities (PIPs) from GWAS summary statistics using Wakefield's ABF method. Run single-trait fine

AbLang — antibody language model for completing and analyzing antibody sequences. Generate residue-level embeddings (res-codings), sequence-level embeddings (seq-codings), restore missing residues fro

adegenet — CRAN R package for multivariate analysis of genetic markers and population genetics. Implements genind and genlight S4 objects for storing individual genotypes and large SNP datasets. Core

Use when working with the Ag100Pest Initiative Snakemake workflows for de novo reference genome assembly and annotation of agricultural pest arthropods. Covers HiFi long-read assembly with hifiasm, Hi

Alleloscope — allele-specific copy number analysis and tumor clonality inference from single-cell multi-omics data (scDNA-seq and scATAC-seq). Estimates allele-specific copy number profiles using SNP

Use when predicting pathogenicity of missense variants with AlphaMissense — Google DeepMind's deep learning model that classifies human missense variants as likely benign, ambiguous, or likely pathoge