Browse Tools

Use when performing neuroimaging analysis in Python with ANTsPy (antspyx). Covers Python-native image registration with ants.registration(), bias field correction with ants.n4_bias_field_correction(),

Use when working with the R package ape for phylogenetic tree I/O, manipulation, plotting, molecular dating, comparative methods, or DNA distance workflows. ape supports Newick and Nexus tree formats,

Use when performing log fold-change (LFC) shrinkage in RNA-seq differential expression analysis with apeglm (Approximate Posterior Estimation for Generalized Linear Model). Integrates with DESeq2 via

Use when working with ArchR for single-cell chromatin accessibility (scATAC-seq) analysis in R. ArchR builds Arrow-backed projects from fragment/BAM inputs, performs doublet scoring, iterative LSI, cl

ARIBA (Antimicrobial Resistance Identification By Assembly) — short-read assembly tool from the Wellcome Sanger Institute for detecting antimicrobial resistance (AMR) genes, virulence factors, and pla

Use when working with the Arrow R package in genomics, transcriptomics, proteomics, or other R/Bioconductor-adjacent pipelines that need Parquet, Feather/IPC, CSV, JSON, or larger-than-memory datasets

Use when working with the ARTIC viral amplicon sequencing command-line pipeline for Oxford Nanopore data. Covers documented `artic minion`, `artic guppyplex`, and `artic_get_models` workflows for prim

Use when working with ASHLAR, whole-slide microscopy stitching, cyclic image registration, CyCIF, CODEX, OME-TIFF mosaics, or plate-mode tile alignment. ASHLAR stitches unstitched microscopy tiles, re

Use when working with ashr (adaptive shrinkage in R) for empirical Bayes shrinkage of effect size estimates in RNA-seq differential expression analysis. ashr fits mixture priors to (betahat, sebetahat

Use this skill for metagenome-atlas (ATLAS) workflows built on Snakemake, including atlas init, atlas init-public, atlas download, and atlas run stages (qc, assembly, binning, genomes, genecatalog, st

autograd — automatic differentiation library for NumPy. Compute exact gradients, Jacobians, Hessians, and higher-order derivatives of Python functions that use NumPy and SciPy. Supports reverse-mode A

Azimuth — reference-based automated cell type annotation for single-cell RNA-seq. Maps a query Seurat object or h5ad dataset onto a curated reference atlas (PBMC, lung, kidney, cortex, heart, bone mar

BaalChIP — Bioconductor R package for detecting allele-specific binding (ASB) in ChIP-seq data. Identifies allelic imbalance at heterozygous SNPs using a Bayesian statistical framework with logistic r

Use when running somatic mutation analysis on cancer whole-genome (WGS), whole-exome (WES), or targeted panel sequencing data with BALSAMIC. Handles tumor-normal and tumor-only workflows, calling SNVs

Bambu — R/Bioconductor package for context-aware transcript discovery and quantification from long-read RNA-seq data (Oxford Nanopore, PacBio). Performs reference-guided isoform reconstruction, novel

Use when working with Bandage-NG (BandageNG), the modernized genome assembly graph visualization tool. Covers loading GFA, FASTG, and Trinity assembly graphs, rendering graph images from the command l

Use when working with BANKSY for spatial transcriptomics clustering that blends each cell's own expression with spatial-neighbor features. Covers SpatialExperiment and SingleCellExperiment pipelines,

Use when working with Basenji, sequence-to-function genomics deep learning, chromosome-scale regulatory activity prediction, variant effect scoring with SAD or SED, or Basenji data/train/test pipeline

Basset — deep convolutional neural network for learning functional activity from genomic DNA sequences. Predicts chromatin accessibility (DNase-seq, ATAC-seq) across 164 cell types from 600 bp DNA win

Use when performing differential expression analysis on RNA-seq or count data using baySeq, an empirical Bayesian framework for DE analysis. Covers full workflow: constructing countData objects, estim

BCFtools ROH — detection of runs of homozygosity (ROH) and autozygosity in diploid genomes from VCF/BCF files. Identify ROH segments using the HMM-based bcftools roh command, estimate inbreeding coeff

BEASTIE (Bayesian Estimation of Allele-Specific Transcription Integrating Expression) — statistical framework for detecting allele-specific expression (ASE) from RNA-seq data. Uses a Bayesian hierarch

BeetleBase is the model organism database for Tribolium castaneum (red flour beetle), covering genome browsing, BLAST searches, gene model retrieval, GO annotation, RNAi phenotype data, and synteny an

Use when working with the R package bigstatsr for large-scale statistical analyses on file-backed big matrices (FBM). bigstatsr stores matrices on disk via memory-mapped .bk files, enabling analyses t

BiocFileCache — R/Bioconductor package for persistent on-disk file caching with SQLite-backed provenance tracking. Manages cached resources via bfcadd(), bfcnew(), bfcquery(), bfcpath(), bfcdownload()

Use when working with Bioconductor BiocGenerics, the R package that defines S4 generic functions shared across the Bioconductor ecosystem. Route users who need to understand how Bioconductor generics

Use when working with Bioconductor AnnotationDbi, the R package that provides a common interface for SQLite-backed annotation packages such as OrgDb, ChipDb, GO.db, and custom AnnotationDb derivatives

BiocParallel — parallel computation framework for Bioconductor workflows in R. Provides a unified interface to multiple parallel backends: MulticoreParam (fork-based, Linux/macOS), SnowParam (socket c

bioframe is a Python library for interval-region manipulation on genomic DataFrames. Use when users need to overlap, merge, subtract, complement, or compute coverage of genomic intervals (BED-like Dat

Bionano Solve — optical genome mapping (OGM) pipeline for de novo genome assembly, hybrid scaffolding, and structural variant (SV) detection using Bionano Genomics nanochannel arrays. Processes BNX ra

BioNetGen and PyBioNetGen workflows for rule-based biochemical modeling in BNGL. Use this skill for BNGL model authoring, network generation, deterministic or stochastic simulation runs, SBML-to-BNGL

Biopython SeqIO — the unified sequence file I/O module for 30+ bioinformatics formats. Read, write, and convert FASTA, FASTQ, GenBank, EMBL, Stockholm, Phylip, NEXUS, PDB-seqres, and more using SeqIO.

Use when working with BirdNET-Analyzer — the deep learning bioacoustics tool for identifying bird species from audio recordings. Covers the BirdNET-Analyzer CLI and Python API: species detection from

BLD-LDAK (SumHer) — LD-adjusted heritability and genetic architecture estimation from GWAS summary statistics. Implements BLD-LDAK, LDAK-Thin, and SumHer models for SNP heritability partitioning, enri

BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) is an R package for genome-wide association studies (GWAS) that scales to millions of individuals and markers. Uses Ba

BMDS (Benchmark Dose Modeling Software) by the U.S. EPA for dose-response modeling and benchmark dose (BMD/BMDL/BMDU) calculation in toxicological risk assessment. Supports dichotomous, continuous, ne

Use this skill for Barcode of Life Data Systems (BOLD) retrieval in R with the ropensci `bold` package. It covers sequence searches, specimen metadata queries, combined specimen-plus-sequence retrieva

Use when working with Brain Connectivity Toolbox (bctpy), graph-theoretic analysis of brain networks, connectome metrics, modularity detection, or network topology measures in Python. bctpy provides c

Neurosynth brain mapping skill for coordinate-based activation mapping, genomics-to-brain spatial integration, and BrainMap-style region annotation. Generates MNI-space probability maps from cognitive

BRASS, CaVEMan, and Pindel — somatic variant calling suite from the Wellcome Sanger Institute Cancer Genome Project. BRASS detects somatic structural variants and chromosomal rearrangements. CaVEMan (

Broad WARP pipelines are a collection of open-source, cloud-optimized pipelines for processing biological data. They are written in WDL and are designed to be run on the Terra platform.

Use when working with BSgenome, Bioconductor whole-genome sequence packages, getBSgenome(), getSeq(), bsapply(), injectSNPs(), genome FASTA export, or masked BSgenome objects in R. BSgenome provides t

Cactus — reference-free whole-genome multiple alignment using progressive decomposition and the cactus graph structure. Produces HAL format alignments for comparative genomics, conservation scoring, l

CAMERA routing skill for metabolomics LC-MS peak annotation and compound spectra extraction. Use this skill when users mention CAMERA, XCMS annotation, peak grouping, pseudo-spectra, isotope peak anno

Use when working with Canvas, Illumina's copy number variant caller for human DNA sequencing. Canvas runs germline, somatic WGS, tumor-normal enrichment, and small-pedigree workflows from aligned BAM

car — Companion to Applied Regression. R package providing Type II/III ANOVA tables via Anova(), variance inflation factors via vif(), general linear hypothesis tests via linearHypothesis(), diagnosti

CARD utilities — query, download, and navigate the Comprehensive Antibiotic Resistance Database (CARD) for antimicrobial resistance (AMR) gene sequences, ARO ontology terms, prevalence data, and resis