Browse Tools

RevBayes — Bayesian phylogenetic inference and evolutionary analysis using graphical probabilistic models and the Rev scripting language. Performs Bayesian MCMC-based phylogenetic tree estimation, div

Rosetta — comprehensive macromolecular modeling suite for protein structure prediction, protein design, docking, loop modeling, and enzyme engineering. Includes RosettaFold for deep-learning structure

SAbDab (Structural Antibody Database) and ANARCI antibody numbering toolkit. Query the curated database of all antibody structures from the PDB with consistent Chothia, IMGT, Kabat, and Martin numberi

Scanorama -- efficient batch correction and integration of heterogeneous single-cell RNA-seq datasets using panoramic stitching. Aligns and merges multiple scRNA-seq experiments via mutual nearest nei

scCRISPR — single-cell multiomics framework for CRISPR perturbation analysis combining scRNA-seq and scATAC-seq readouts. Built on the MPAL-Single-Cell-2019 codebase from the Greenleaf Lab, it integra

scGen — deep learning framework for predicting single-cell perturbation responses using variational autoencoders. Predicts how cells respond to unseen conditions (drug treatment, genetic knockout, dis

Use when working with scPrediXcan — a TWAS (Transcriptome-Wide Association Study) framework that extends PrediXcan to single-cell resolution using sc-eQTL prediction models. Maps GWAS loci to cell-typ

Use when working with scvi-hub — scvi-hub — the HuggingFace Hub integration

Sickle — sliding-window quality trimming tool for short-read Illumina FASTQ data. Trims low-quality bases from 3' and 5' ends using a windowed adaptive algorithm. Supports paired-end (pe) and single-e

softImpute — R package for matrix completion via iterative soft-thresholded SVD with nuclear-norm regularization. Implements ALS and SVD algorithms for imputing missing entries in large incomplete mat

CmdStan — command-line interface to the Stan probabilistic programming language for Bayesian statistical modeling and high-performance inference. Compiles Stan programs (.stan) to C++ executables via

STdeconvolve — reference-free cell-type deconvolution for spatial transcriptomics using Latent Dirichlet Allocation (LDA). Decomposes multi-cellular spatial pixels into cell-type proportions and trans

TCGA/GDC tools — NCI Genomic Data Commons Data Transfer Tool and API client for downloading cancer genomics data from TCGA, TARGET, CGCI, and related programs. Provides high-performance file downloads

Use when performing Transcriptome-Wide Association Studies (TWAS) with TIGAR, a nonparametric Bayesian tool from Yang Lab for training gene expression prediction models and testing gene-trait associat

TileDB for dense and sparse multi-dimensional arrays, data management, provenance-aware storage, and cloud/hybrid object-store access. Use this skill when users ask about TileDB Embedded, TileDB-Py, a

TMB/MSI analysis tools — Tumor Mutational Burden (TMB) estimation and Microsatellite Instability (MSI) detection from paired tumor-normal sequencing data. Covers MSIsensor for MSI scoring from BAM fil

Trackpy is a Python package for fast, Pythonic particle tracking in 2D and 3D image sequences. Implements the Crocker-Grier algorithm to locate bright features (particles, colloids, cells, droplets) a

Use when working with TreeMix for population genetics admixture graph inference, including input preparation from PLINK or VCF files, running maximum-likelihood tree fitting with migration events, and

ukbREST — a REST API server for UK Biobank (UKB) phenotype data that enables programmatic querying of biobank-scale phenotype fields via HTTP endpoints. Backed by PostgreSQL, it supports phenotype ext

Weights & Biases (wandb) — ML experiment tracking, hyperparameter sweeps, artifact versioning, and collaborative model management platform. Log training metrics, gradients, system stats, and media (im

Xarray — N-dimensional labelled arrays and datasets for scientific Python. Provides a toolkit for reading, writing, and manipulating multi-dimensional arrays with labels (dimensions, coordinates, attr

X!Tandem — open-source proteomics search engine for matching tandem mass spectra (MS/MS) to peptide sequences in protein databases. Performs database searching with configurable scoring, supports post

Tools and workflows for accessing, querying, and analyzing data from the 1000 Genomes Project (1KGP) — the largest public catalog of human genetic variation with whole-genome sequences from 3,202 indi

10x Genomics — commercial platform for single-cell and spatial genomics assays including Chromium single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq, single-cell multiome (RNA+ATAC), Visium spatial

Arima-HiC mapping pipeline — shell-based workflow for aligning and processing Hi-C data generated with Arima Genomics proximity ligation kits. Maps paired-end FASTQ reads with BWA-MEM using Hi-C-speci

Benchmark and compare bioinformatics tools for a given analysis task using published benchmark data (accuracy, runtime, memory), PrecisionFDA and CAMI challenge results, bc7score community metrics, an

Use when querying ClinGen — the Clinical Genome Resource — for expert-curated gene-disease validity classifications, variant pathogenicity interpretations, dosage sensitivity assessments, and clinical

Use when working with cram-tools — CRAM tools — reference-based compression

dbSNP tools — NCBI toolkit for querying, downloading, and processing dbSNP variant data. Look up rsIDs via REST API, bulk-download VCF/JSON releases, annotate variant lists with allele frequencies and

EBSeq is an R/Bioconductor package implementing an empirical Bayes hierarchical model for identifying differentially expressed (DE) genes and isoforms in RNA-seq experiments. It supports both two-cond

Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem

FD — CRAN R package by Laliberté, Legendre, and Shipley for measuring functional diversity (FD) from multiple traits. Implements the distance-based multidimensional FD framework (functional richness F

FirePy — ECMWF's Python toolbox for global wildfire risk forecasting and fire emissions analysis. Covers the AI-Probability-of-Fire (PoF) XGBoost framework for 1 km / 10-day fire danger probability, C

FlyBase is the primary model-organism knowledgebase for Drosophila melanogaster and related Drosophila species. Use this skill when users need FlyBase gene records, allele and phenotype data, transgen

Franklin — web-based clinical variant interpretation platform by Genoox for ACMG/AMP-based pathogenicity classification of SNVs, indels, and CNVs. Provides a community-curated variant database, REST A

GA4GH Schemas — the Global Alliance for Genomics and Health data models and APIs for standardized genomic data exchange. Defines Protobuf/JSON schemas for Reads (SAM-equivalent), Variants (VCF-equival

Getz Lab tools (ABSOLUTE, MuTect/MuTect2) from the Broad Institute for cancer genomics. ABSOLUTE infers tumor purity, ploidy, and absolute copy numbers from segmented copy number data. MuTect2 (GATK4)

htsget — GA4GH REST streaming API for accessing genomic reads and variants from remote servers. Fetch BAM, CRAM, VCF, or BCF data by region using HTTP ticket-based retrieval. Supports Bearer token aut

Hymenoptera Genome Database (HGD) — community resource for ant, bee, and wasp genome sequences, gene annotations, and comparative genomics. Provides BLAST search, genome browsers (JBrowse), gene expre

INSaFLU-TELEVIR is a web-based (and locally installable) bioinformatics suite for viral genomic surveillance and metagenomics-based virus detection. It processes Illumina, Ion Torrent, and Oxford Nano

UCSC Kent Utilities — command-line toolkit for genome coordinate conversion (liftOver), binary genome formats (.2bit, BigBed, BigWig), BLAT alignment, annotation format interconversion (GTF↔GenePred),

Microreact — web-based visualization platform for genomic epidemiology that combines interactive phylogenetic trees, geographic maps, and timelines with metadata tables synchronized through client-sid

MIDORI Reference 2 (MIDORI2) is a curated reference database of eukaryotic mitochondrial DNA and amino acid sequences used for taxonomic assignment of environmental and metabarcoding samples. It provi

MissForest is a non-parametric imputation method for handling missing values in datasets with mixed-type data (continuous and categorical) based on Random Forests. It iteratively imputes missing value

mvabund is an R package providing a model-based approach to analyzing multivariate abundance data in ecology. It offers tools for data visualization, fitting predictive generalized linear models (GLMs

PLIP (Protein-Ligand Interaction Profiler) — rule-based detection, profiling, and visualization of non-covalent protein-ligand interactions in 3D structures. Identifies hydrogen bonds, hydrophobic con

RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i

Scrublet — Python toolkit for computational identification of cell doublets in single-cell RNA-seq data. Simulates synthetic doublets from observed transcriptomes and scores cells via k-nearest-neighb

Search publications for a bioinformatics tool — find peer-reviewed papers that use, cite, or benchmark a tool using PubMed E-utilities, CrossRef REST API, and OpenAlex scholarly graph. Aggregates cita

UCSC Table Browser API — programmatic access to the UCSC Genome Browser's track data via REST endpoints. Retrieve genomic sequences, annotation tracks, gene models, conservation scores, and regulatory