Browse Tools

BIMS (Biobank Information Management System) — open-source platform for biorepository sample lifecycle management. Tracks biological specimens (blood, tissue, DNA, plasma) from collection through stor

Buildpacks (pack CLI) converts source code into OCI images without writing Dockerfiles by orchestrating Cloud Native Buildpacks lifecycle phases. Use this skill when users ask about pack build, builde

Seqera Platform (formerly Nextflow Tower) — cloud orchestration and monitoring platform for Nextflow pipelines. Provides the tw CLI for launching pipelines, managing compute environments (AWS Batch, G

Use when working with 3D Slicer for medical image visualization, segmentation, registration, or DICOM processing. Covers loading DICOM series, volumetric segmentation with Segment Editor, image regist

adehabitatHR (CRAN) home-range estimation for animal telemetry and relocation data in R. Routes users to Minimum Convex Polygon (mcp), kernel utilization distributions (kernelUD), Brownian bridge home

adjustText — Python library for automatically adjusting matplotlib text label positions to prevent overlapping in scatter plots, genomic manhattan plots, volcano plots, and any figure with dense point

AF-Multimer — AlphaFold-Multimer for protein complex structure prediction. Predicts 3D structures of heteromeric and homomeric protein complexes from multi-chain FASTA using AlphaFold v2.3.x with the

AllenSDK is the Python toolkit for accessing Allen Institute for Brain Science datasets including brain atlases, cell types electrophysiology, calcium imaging (Brain Observatory), RNA-seq transcriptom

AlphaFold2 — deep learning system for predicting 3D protein structures from amino acid sequences with atomic-level accuracy. Uses multiple sequence alignments (MSAs) and an attention-based Evoformer a

Routing skill for amt (Animal Movement Tools) in R. Use when users need animal telemetry preprocessing, track and step construction, sampling-rate checks, home-range estimation (MCP/KDE/AKDE/LoCoH), o

Use when processing environmental DNA (eDNA) multilocus metabarcode data with the Anacapa Toolkit. Covers sequence QC and ASV parsing with DADA2, taxonomy assignment with Bowtie 2 plus BLCA, CRUX refe

AnnData on-disk workflows for large single-cell and spatial omics datasets using .h5ad and Zarr stores. Covers memory-aware reading with backed mode, lazy access with anndata.experimental.read_lazy, d

Apache Arrow — cross-language columnar in-memory analytics format and ecosystem. Provides zero-copy IPC between Python, R, C++, Java, Go, and Rust via shared memory and the C Data Interface. Use for:

ArviZ — Python library for exploratory analysis of Bayesian models providing posterior visualization (trace, forest, pair, posterior plots), diagnostics (R-hat, ESS, MCSE, BFMI), model comparison (LOO

Use when performing computational astrobiology analyses — genomic and metabolic characterization of extremophile microorganisms, biosignature detection in metagenomic datasets, and planetary habitabil

Autoreject is a Python library for automated rejection and repair of bad EEG and MEG epochs. It uses cross-validation to find optimal peak-to-peak amplitude rejection thresholds per channel, then eith

Bayesian Calibration for MPRA experiments. Normalizes DNA/RNA count tables, estimates calibrated activity scores with posterior distributions, handles low-count sequences and replicate comparison.

Benchling is a cloud-based life sciences R&D platform for molecular biology, electronic lab notebooks (ELN), LIMS, and data management. Provides REST API and Python SDK for programmatic access to sequ

BERN2 (Biomedical Entity Recognition and Normalization 2) is a biomedical NLP tool for named entity recognition and normalization in free text and PubMed abstracts. Identifies and normalizes genes, di

'Use when working with bio-tool-search — bio-tool-search — search 47,000+

Use when working with BioBERT — a pre-trained biomedical language representation model for biomedical text mining. Covers fine-tuning and inference for Named Entity Recognition (NER), Relation Extract

Use when working with biomaRt, BioMart queries in R, Ensembl annotation retrieval, cross-dataset identifier mapping, or annotation lookups through Bioconductor. biomaRt connects R to BioMart services

biomod2 species distribution and ecological niche modeling in R. Use this skill for BIOMOD_FormatingData preparation, pseudo-absence strategies, BIOMOD_Modeling calibration, BIOMOD_Projection and BIOM

BluePyOpt — Blue Brain Python Optimisation Library for single-neuron compartmental model optimization using evolutionary algorithms (CMA-ES, NSGA-II). Fits biophysical Hodgkin-Huxley models to electro

BPCells is a high-performance toolkit for large single-cell RNA-seq and ATAC-seq datasets. Use it when the user mentions BPCells, disk-backed sparse matrices, bitpacked single-cell storage, large 10x

BPNet — deep learning framework for learning base-resolution regulatory sequence features from genomics assays (ChIP-seq, ATAC-seq, CUT&RUN). Uses dilated convolutional neural networks to predict TF b

Breeder routing skill for genomic selection, genome-wide prediction, and quantitative genetics in plant and animal breeding. Use this skill when users mention breeder, genomic selection, GBLUP, G-BLUP

Converts statistical model objects in R into tidy tibbles. The core functions are `tidy()` for coefficient-level output, `glance()` for model-level summaries, and `augment()` for observation-level dat

BugBase is a tool for analyzing microbiome data to predict organism-level phenotypes. It is particularly useful for soil science and terrestrial ecology, allowing users to analyze their microbiome sam

Cartopy is a cartographic Python library for geospatial plotting with Matplotlib. Use this skill for map projections, coordinate reference system transforms, Natural Earth features, shapefile-driven v

Use when working with CATALYST for mass-cytometry or flow-cytometry analysis in R/Bioconductor, including preprocessing with prepData, normCytof, assignPrelim, estCutoffs, applyCutoffs, computeSpillma

Use when running CAUSE (Causal Analysis Using Summary Effect estimates) for Mendelian randomization with GWAS summary statistics. CAUSE distinguishes causal effects from correlated and uncorrelated pl

CDAT (Climate Data Analysis Tools) — an open-source, Python-based software system for climate data analysis and visualization. Built for handling large climate datasets, CDAT integrates data access, a

CDO (Climate Data Operators) is a collection of command-line operators for manipulating and analyzing Climate and Forecast (CF) data. Primary use cases include data processing, statistical analysis, a

CellBender removes ambient RNA contamination and technical noise from droplet-based single-cell RNA-seq data using a deep generative model (VAE). Processes raw 10x Genomics feature-barcode matrices to

Use when working with CellNOptR (Cell Network Optimizer in R), a Bioconductor package for training logic-based signaling network models to phosphoproteomic or biochemical data. Covers Prior Knowledge

Cellranger-arc — 10x Genomics pipeline for processing Multiome ATAC + Gene Expression data from the Chromium Multiome kit. Aligns FASTQ reads, calls peaks, quantifies gene expression and chromatin acc

Query the CZ CELLxGENE Census (61M+ cells) programmatically via TileDB-SOMA. Use when you need single-cell expression data across tissues, diseases, or cell types from the largest curated atlas. Suppo

CERVUS is a software package for parentage analysis and individual identification using codominant genetic markers (microsatellites, SNPs). Applies maximum-likelihood LOD scores and simulation-based c

cfgrib is a Python interface for reading GRIB1/GRIB2 files through ecCodes and mapping them to xarray datasets following CF conventions. Use this skill for weather and climate workflows that need engi

Use when working with chanjo — chanjo — clinical genomics coverage analysis

Use when working with chemCPA for single-cell perturbation response modeling, especially prediction of cellular responses to unseen drugs, transfer learning from bulk to single-cell perturbation data,

ChemProp — directed message passing neural network (D-MPNN) for molecular property prediction from SMILES. Train classification, regression, or multiclass models with atom/bond featurization, scaffold

Use when working with chromhmm — chromHMM — Java-based tool for learning

Use when working with cistem — cisTEM — single-particle cryo-EM data

CLAM (Clustering-constrained Attention Multiple instance learning) — weakly supervised computational pathology framework for whole slide image (WSI) classification and survival analysis. Processes gig

CliMetLab is an ECMWF Python toolkit for unified weather and climate data access. Use this skill when workflows need `climetlab.load_source(...)`, `climetlab.load_dataset(...)`, cache/settings control

Use this skill for COBRApy workflows in constraint-based metabolic modeling, including loading SBML/JSON/YAML genome-scale models, running FBA/pFBA/FVA, configuring growth medium constraints, and vali

Use this skill for COBRApy workflows in constraint-based metabolic modeling, including loading SBML/JSON/YAML genome-scale models, running FBA/pFBA/FVA, configuring growth medium constraints, and vali

Use when working with CodonTransformer — a BigBird transformer model for multi-species codon optimization. Converts protein amino acid sequences into DNA coding sequences with organism-specific codon