Browse Tools

Nanopore direct RNA sequencing — end-to-end analysis of native RNA reads from Oxford Nanopore devices. Basecalling with Dorado, QC with NanoPlot and NanoStat, alignment with minimap2, isoform quantifi

plyranges is an R/Bioconductor package providing a tidyverse-style interface for genomic interval manipulation via GRanges and IRanges. Use when users need to filter, join, resize, or summarise genomi

PrimerBLAST is an NCBI web tool that combines Primer3 for PCR primer design with BLAST-based specificity checking against NCBI databases. Designs primers for a target sequence, checks them for off-tar

Tree of Life pipelines from the Wellcome Sanger Institute (sanger-tol) are a suite of Nextflow/nf-core pipelines for biodiversity genomics: genome assembly (genomeassembler), assembly validation (tree

UniProt REST API tools — programmatic access to UniProtKB, UniRef, and UniParc protein databases via the REST API at rest.uniprot.org. Supports protein search, entry retrieval, sequence download, ID m

valr is an R package for genomic interval arithmetic using a tidy, tidyverse- compatible interface. Use when users need to intersect, merge, subtract, complement, or annotate genomic intervals in BED-

AOP-Wiki (Adverse Outcome Pathway Wiki) is the authoring and discovery interface for browsing, searching, exporting, and citing AOP knowledgebase content including AOPs, Key Events (KEs), Key Event Re

Bioconda — community-driven Conda channel providing 12,000+ bioinformatics packages with pinned dependencies and reproducible environments. Supports recipe creation, environment management, containeri

Use when working with SpikeInterface — the unified Python framework for extracellular electrophysiology spike sorting. Covers loading recordings from 30+ formats (NWB, OpenEphys, Maxwell, Intan, MDA,

AnimalGenome.org data-access skill for livestock genomics workflows using Animal QTLdb and CorrDB. Routes users to REST-style API usage (`iinfo`, `iquery`, `ifetch`), species-level QTL and trait-corre

BayesSpace for spatially-resolved clustering and resolution enhancement of spatial transcriptomics data. Performs Bayesian spatial clustering with a Potts smoothing prior on 10x Visium and Slide-seq d

Use when predicting clinical pathogenicity of missense variants, scoring nonsynonymous SNVs for disease relevance, filtering rare variants by pathogenicity probability, annotating VCF files with ClinP

CompTox Chemicals Dashboard is the U.S. EPA's publicly accessible resource for chemical information, identity resolution, toxicity data, and DSSTox database access. Use this skill for chemical search

Cytoscape.js — JavaScript graph theory library for network visualization and analysis in the browser and Node.js. Renders interactive biological networks, protein-protein interaction graphs, pathway d

GATK ASEReadCounter counts allele-specific expression (ASE) read coverage at heterozygous SNP sites from RNA-seq BAM files. Use for allelic imbalance analysis, ASE quantification, imprinting studies,

"GRAPE — Graph Representation learning for Analysis and Predictions and Evaluations. Use for GNN-based link prediction, node classification, graph embedding, pathway analysis, PPI network analysis, dr

InsectBase — comprehensive web database for insect genome sequences, gene annotations, and comparative genomics data covering 138+ insect species. Provides genome assemblies (FASTA), structural annota

LD Score Regression (LDSC) for estimating SNP heritability, genetic correlation, and partitioned heritability from GWAS summary statistics. Use when working with ldsc, LD score regression, heritabilit

LepBase — versatile, scalable search engine and genome database for Lepidoptera (butterflies and moths) assemblies and genomic features. Provides genome browser, BLAST sequence search, REST API for ge

MAGMA (Multi-marker Analysis of GenoMic Annotation) for gene-level and gene-set analysis of GWAS summary statistics. Use when performing gene analysis from SNP p-values, gene-set enrichment testing, c

Mothur is an open-source bioinformatics platform for microbial ecology analysis. Provides tools for 16S/18S/ITS amplicon sequence processing, OTU clustering, phylotype classification, ASV generation,

mpralm is an R/Bioconductor package for differential activity analysis of Massively Parallel Reporter Assays (MPRA). It uses a limma-voom-style framework to compare RNA barcode counts to DNA barcode c

Use when working with mTAGs, metagenomics rRNA-based taxonomic profiling, 16S 18S 23S 28S marker gene classification from shotgun reads, SSU rRNA community profiling, SILVA-based metagenome classifica

nilearn for machine learning and statistical analysis of neuroimaging data. Use when working with fMRI, brain connectivity, functional parcellation, GLM contrasts, ICA decomposition, NIfTI image manip

PLINK/SEQ — open-source C/C++ library and command-line tool (pseq) for working with human genetic variation data from large-scale resequencing projects. Use when working with VCF loading, variant filt

scGNN — single-cell Graph Neural Network framework for scRNA-seq analysis. Uses graph autoencoders and graph convolutional networks for cell clustering, expression imputation, cell-type inference, and

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SMR (Summary-data-based Mendelian Randomization) for testing pleiotropic associations between molecular traits (eQTL, mQTL, sQTL) and complex traits using GWAS summary statistics. Includes HEIDI test

SPARK for identifying spatially variable genes in spatial transcriptomics data. Uses generalized linear spatial models with penalized quasi-likelihood (PQL) and multiple spatial kernels to test for sp

Supernova for de novo whole-genome assembly from 10x Genomics Chromium linked-read data. Use when assembling diploid genomes, generating pseudohaplotype sequences, producing megabubble assemblies, or

TDFragMapper is a Windows GUI application for evaluating top-down proteomics fragmentation experiments by combining preassigned fragment ions from multiple MS/MS runs on a single protein sequence map.

UCSC Genome Browser — web-based genome annotation browser providing access to reference genome assemblies, gene predictions, comparative genomics, variation, regulation, and expression data across hun

Use this skill for Apptainer/Singularity container workflows in HPC and scientific computing, including pulling OCI images, building SIF artifacts, running commands with bind mounts and environment va

Use when working with BE-Hive, the Shen lab base-editing outcome predictor distributed through the `be_predict_bystander` repository and the crisprbehive.design web app. BE-Hive predicts bystander edi

Use this skill for BinderHub and mybinder-style reproducible interactive environments built from Git repositories. Triggers on Binder, BinderHub, mybinder, repo2docker, launch badges, build logs, Kube

Bio-ORACLE (Oceanographic Reconstructions and Climate-Linked Ecology) is a global dataset and toolkit for marine biology and oceanography. It provides geospatial data products for temperature, salinit

A collection of tools for accessing, analyzing, and downloading data from the Biobank Japan project. Provides functionalities for querying phenotypes, genotypes, and other omics data.

BiocCheck (Bioconductor) quality gate for R package submissions and release maintenance. Use when validating Bioconductor package compliance after `R CMD check`, triaging BiocCheck ERROR/WARNING/NOTE

Biomechanics computational analysis skill covering motion capture data processing, musculoskeletal modeling, and gait analysis using Python tools (pyomeca, ezc3d, opensim-core). Analyze C3D motion cap

Bioprocess engineering computational tools for bioreactor design, fermentation kinetics, metabolic flux analysis, and bioprocess scale-up. Model bioreactor dynamics (batch, fed-batch, continuous/CSTR)

Black is the uncompromising Python code formatter used to enforce consistent style with minimal configuration. Use this skill when users ask to format Python code, run black in CI, configure pyproject

Use when working with Bokeh for interactive Python visualization, web-native plotting, dashboards, linked selections, streaming updates, and Bokeh server applications. Covers `bokeh.plotting` glyph wo

Brainnetome Atlas — a human brain parcellation of 246 subregions (210 cortical + 36 subcortical) derived from connectivity-based parcellation using diffusion MRI tractography and resting-state fMRI. P

Brian2 — Python simulator for spiking neural networks (SNNs). Define neuron models as systems of differential equations (integrate-and-fire, Hodgkin-Huxley, AdEx, or custom), connect populations via S

brms (Bayesian Regression Models using Stan) is an R package providing a high-level formula interface to Stan for Bayesian multilevel, nonlinear, and distributional regression models. Supports linear,

cairosvg — Python library and CLI for converting SVG files to PNG, PDF, PostScript (PS), and EPS formats using the Cairo graphics library. Designed for publication-quality figure export from vector gr

CausalImpact — Google's R package for causal inference on time series using Bayesian structural time-series (BSTS) models. Estimate the causal effect of an intervention (ad campaign, policy change, tr