Browse Tools

Use when working with CARMA — Causal Variants Identification in Associated Regions using MAP Approximation. Bayesian fine-mapping tool for GWAS summary statistics that identifies likely causal variant

Use when working with CARNIVAL (CAusal Reasoning for Network Identification using Integer VALue programming), an R package for inferring causal signaling network topologies from transcriptomic data. C

CarveMe builds genome-scale metabolic models (GEMs) for microbes from protein or DNA FASTA, RefSeq accessions, or eggNOG annotations, then supports media-aware gap filling and microbial community mode

CAVIAR (CAusal Variants Identification in Associated Regions) is a statistical fine-mapping tool that identifies causal variants in GWAS loci using Z-scores and linkage disequilibrium (LD) matrices. U

CellGenIT tools from the Wellcome Sanger Institute Cellular Genetics Informatics team. Suite of Python utilities for single-cell genomics including sinto (fragment file generation from BAM), cellhint

CellProfiler — open-source image analysis software for quantitative measurement of cell phenotypes from microscopy images. Supports high-content screening, cell segmentation (IdentifyPrimaryObjects, I

cellSNP-lite — fast C-based tool for genotyping single cells and bulk samples at known or de-novo SNP sites from BAM/SAM files. Generates sparse genotype matrices (AD/DP/OTH counts) in VCF/BCF format

celltypist — automated cell type annotation for single-cell RNA-seq data using pre-trained logistic regression models from a curated model zoo. Use for: cell type classification, immune cell annotatio

cellxgene — interactive single-cell data explorer from the Chan Zuckerberg Initiative. Launch a local browser-based visualizer for any AnnData (.h5ad) file: pan-zoom UMAP/PCA plots, gene expression ov

Chromap — ultrafast chromatin accessibility and Hi-C read alignment tool for single-cell and bulk ATAC-seq, CUT&Tag, and Hi-C data. Performs alignment, deduplication, and fragment file generation in a

Use when working with ChromBPNet — a bias-factored deep learning framework for modeling chromatin accessibility from DNA sequence using ATAC-seq or DNase-seq data. Covers the full ChromBPNet pipeline:

circlize — R package for circular visualization including Chord diagrams, Circos plots, and genomic circular tracks. Create circular layouts with circos.initialize(), add tracks with circos.track(), a

CIViC (Clinical Interpretation of Variants in Cancer) — comprehensive knowledgebase for cancer genomic variant interpretation. Provides expert-curated clinical evidence linking cancer mutations to tre

CliqueSNV reconstructs minority viral haplotypes and calls low-frequency SNVs from noisy Illumina and PacBio read alignments. Use this skill when users ask about quasispecies assembly, viral haplotype

Use this skill for compleasm genome assembly completeness assessment. Route here when users ask about BUSCO-based assembly evaluation, miniprot-based completeness scoring, lineage dataset selection fo

Compound Discoverer routing skill for metabolomics and lipidomics LC-MS/MS data processing and compound identification using Thermo Fisher Scientific Compound Discoverer software. Use this skill when

CompoundDb routing skill for metabolomics compound annotation database creation and management. Use this skill when users mention CompoundDb, CompDb, EuracBiomedicalResearch CompoundDb, creating metab

Connectome Workbench — HCP neuroimaging suite for surface-based and volume-based brain connectivity analysis. Provides wb_command CLI for CIFTI, GIFTI, and NIFTI manipulation: smoothing, parcellation,

Use when working with Conos (Clustering On Network Of Samples), the R package for joint analysis of multiple single-cell RNA-seq and spatial transcriptomics datasets. Covers building joint k-nearest-n

Use this skill when the user needs Control-FREEC (control-FREEC, FREEC, copy-number calling, CNA segmentation, LOH/BAF estimation, or exome copy-number analysis from BAM/pileup). Route requests for FR

COSMIC (Catalogue Of Somatic Mutations In Cancer) is the authoritative curated database of somatic mutations driving human cancer, maintained by the Wellcome Sanger Institute. Use this skill for query

CPSR (Cancer Predisposition Sequencing Reporter) — Python tool for clinical interpretation of germline variants in cancer predisposition genes. Generates interactive HTML reports with ACMG/AMP variant

A software program to generate curated reference databases for metabarcoding sequencing data. CRABS automates the creation of reference databases by downloading, importing, and curating data from mult

'Use when working with cryodrgn — cryoDRGN — deep variational autoencoder

Use when merging multiple Cufflinks transcript assemblies into a unified transcriptome for downstream differential expression analysis with Cuffdiff. Covers the full Cuffmerge workflow: creating assem

Pegasus is a Python package for analyzing and visualizing large-scale single-cell and single-nucleus RNA-seq data, developed by the Broad Institute's Li Lab. Performs QC filtering, normalization, PCA,

Use when working with CutITS, the command-line tool for extracting and trimming ITS (Internal Transcribed Spacer) regions from fungal amplicon sequencing reads. Covers ITS1, ITS2, and full ITS extract

CUT&RUNTools 2.0 — end-to-end analysis pipeline for CUT&RUN and CUT&TAG chromatin profiling experiments. Handles adapter trimming (Trimmomatic), spike-in normalization, Bowtie2 alignment with size-sel

CyTOF workflow — differential discovery in high-dimensional mass cytometry data using the CATALYST R/Bioconductor package. Covers the full CyTOF analysis pipeline: bead-based normalization, single-cel

Use when performing Bayesian fine-mapping of GWAS loci with DAP-G (Distributed Adaptive Posterior Sampling with Genomic annotations). DAP-G computes posterior inclusion probabilities (PIPs) and credib

dartR -- R package for population genomics analysis of SNP data generated by Diversity Arrays Technology (DArT) genotyping. Handles DArT-specific quality filtering (reproducibility, call rate, minor a

Use when working with Datashader for large-scale visualization, rasterizing point/line/polygon/mesh data to fixed-size grids, or building high-density scientific plots without overplotting. Covers `da

Use when working with data.table — the high-performance R package for fast data manipulation, aggregation, and file I/O on large datasets. data.table extends data.frame with a concise DT[i, j, by] syn

dDocent — bash-based RADseq population genomics pipeline for ddRAD, 2bRAD, and ezRAD data. Performs quality trimming (Trimmomatic), de novo or reference-guided assembly (CD-HIT / Rainbow / BWA-MEM), S

DeepConsensus — Google's gap-aware sequence transformer for improving PacBio CCS (HiFi) read accuracy post-basecalling. Use for: polishing PacBio long reads, reducing insertion/deletion errors in CCS

DeepLoc predicts the subcellular localization of eukaryotic proteins from sequence using deep learning. Use when users need to annotate protein subcellular location (nucleus, cytoplasm, extracellular,

Use when working with DeepRVAT — a deep learning framework for rare variant association testing (RVAT) that learns gene-level embeddings from rare variant annotations using an auto-encoder, then tests

DeepSEA — deep learning framework for predicting chromatin effects of sequence alterations at single-nucleotide resolution. Trains convolutional neural networks on 919 chromatin features (TF binding,

DeepSqueak is a deep learning-based tool for automated detection and classification of ultrasonic vocalizations (USVs) in rodents (mice, rats). Uses YOLO object detection on spectrograms to identify a

Use when working with DeepSTARR — a deep learning CNN model for predicting enhancer activity from DNA sequence using STARR-seq training data. Covers sequence-to-activity prediction for developmental (

Use when working with DeepTrio, Google's deep-learning variant caller for parent-child trio sequencing data. Calls SNPs and indels jointly from proband, parent1, and parent2 BAM files aligned to a ref

DelayedArray — core Bioconductor infrastructure for out-of-core array computation. Wraps any array-like seed (HDF5, TENxMatrix, in-memory) behind a unified delayed-operation tree so downstream code wo

DELLY — Structural variant discovery tool that uses paired-end and split-read analysis to detect deletions, tandem duplications, inversions, translocations, and copy-number variants from short-read an

densMAP — density-preserving dimensionality reduction for visualization. Augments UMAP with a density-correlation regularizer that preserves local density information from high-dimensional data in the

DepMap/CCLE tools for cancer dependency mapping and cell line omics analysis. Access CRISPR gene effect scores (Chronos/CERES), RNAi dependency data, gene expression (TPM), copy number alterations, so

Use when running DEsingle for two-group differential expression analysis on single-cell RNA-seq raw count matrices in R/Bioconductor. Covers DEsingle() model fitting with zero-inflated negative binomi

DGIdb (Drug Gene Interaction Database) — query, filter, and analyze drug-gene interactions from 40+ aggregated sources. Provides GraphQL and REST APIs for gene druggability lookup, drug-target interac

DIA-NN — automated software suite for data-independent acquisition (DIA) proteomics data processing. Uses deep neural networks for peptide retention time, ion mobility, and fragmentation prediction to

Use when working with diffcyt for differential discovery in high-dimensional cytometry (flow, CyTOF, or oligo-tagged cytometry). diffcyt combines high-resolution FlowSOM clustering with moderated stat

DisGeNET is a comprehensive knowledge platform integrating and standardizing information on disease-associated genes and variants from multiple sources (curated databases, literature, animal models).