Browse Tools

Use when working with DoRothEA or CollecTRI for transcription factor activity inference, gene regulatory network analysis, or regulon-based enrichment in single-cell or bulk RNA-seq data. DoRothEA pro

DOSE — Disease Ontology Semantic and Enrichment analysis R/Bioconductor package for gene set enrichment against disease ontologies. Performs over-representation analysis (ORA) and gene set enrichment

DoubletFinder — R package for detecting neotypic doublets in single-cell RNA-seq data using artificial nearest neighbor (pANN) scoring. Interfaces with Seurat objects (v2–v5) to identify heterotypic d

dplyr — grammar of data manipulation R package from the tidyverse. Provides consistent, expressive verbs for filtering rows, selecting columns, mutating values, summarising groups, and joining tables.

Use when working with dream, variancePartition differential expression in R, repeated measures RNA-seq analysis, mixed model differential expression, or linear mixed model testing across biological re

dreamlet is a Bioconductor R package for scalable pseudobulk differential expression analysis of single-cell and spatial RNA-seq data using mixed models. It handles repeated measures and complex desig

Use when working with DropletUtils for processing droplet-based single-cell RNA-seq data from 10x Genomics CellRanger output. DropletUtils provides read10xCounts() for loading MEX/HDF5 output, emptyDr

Use when working with DSS (Dispersion Shrinkage for Sequencing) — a Bioconductor R package for differential methylation analysis of bisulfite sequencing data (WGBS, RRBS). Covers the full DSS pipeline

Duplex-Seq-Pipeline (duplex-seq-tools) is a Snakemake-based pipeline for ultra-accurate error-corrected sequencing using duplex sequencing (DS). Removes PCR and sequencing errors by collapsing read fa

EAGER2 / nf-core/eager — reproducible Nextflow pipeline for ancient DNA (aDNA) and palaeogenomics. Handles adapter trimming with AdapterRemoval2, read merging, low-complexity filtering, mapping with B

eCAVIAR — GWAS and eQTL colocalization tool that computes the Colocalization Posterior Probability (CLPP) for each variant to identify shared causal variants across two traits. Extends CAVIAR to joint

ECMWF API Client — Python library for programmatic access to the European Centre for Medium-Range Weather Forecasts (ECMWF) data archives. Enables retrieval of weather, climate, and atmospheric compos

eemont extends the Google Earth Engine Python API with 250+ spectral index computation (spectralIndices), automatic cloud masking (maskClouds), scale and offset correction (scaleAndOffset), time serie

elPrep is a high-performance, multi-pass-fused preprocessing tool for SAM/BAM/CRAM files in NGS variant-calling pipelines. Use when users need single-pass duplicate marking, base quality score recalib

EMBL-EBI (European Bioinformatics Institute) — access bioinformatics databases and analysis services from EMBL-EBI including EBI Search for cross-database discovery, EMBL-EBI Tools Job Dispatcher for

ENCODE DCC ATAC-seq pipeline — ENCODE consortium-standard WDL/Cromwell pipeline (run via Caper) for processing bulk ATAC-seq data from FASTQ through alignment, deduplication, peak calling (MACS2), IDR

Enformer — transformer-based deep learning model from DeepMind that predicts gene expression, chromatin accessibility, histone modifications, and TF binding from 196,608 bp raw DNA sequence at 128 bp

ENIGMA Toolbox — Python/MATLAB framework for cross-disorder neuroimaging and genomics analysis using ENIGMA consortium summary statistics. Loads precomputed subcortical and cortical disorder effect si

Ensembl Regulation (ensembl-funcgen) is the EMBL-EBI framework for annotating functional regulatory genomic elements including regulatory features, enhancers, promoters, transcription factor binding s

Ensembl REST API — HTTP/JSON web service for programmatic access to Ensembl genomic data without installing local databases. Supports gene/transcript/protein lookup by stable ID or gene symbol, sequen

Use when working with Ensembl VEP (Variant Effect Predictor) to annotate SNPs, indels, and structural variation with gene, transcript, and protein-level consequences. Supports VCF, HGVS, and coordinat

Ensembl Vet Tools — bioinformatics resources for veterinary and livestock genomics using the Ensembl infrastructure. Covers genome browsing for FAO Priority Livestock Species (cattle, pig, chicken, sh

Use when working with Epiclomal — a Python tool for probabilistic clustering of sparse single-cell DNA methylation data to infer epigenetic clonal structure. Covers the full Epiclomal pipeline: prepar

Use when working with eQTL Catalogue — a uniformly processed, open-access resource of expression quantitative trait loci (eQTL) summary statistics from 100+ studies across bulk tissues, primary cell t

ESM-2 — Meta AI protein language model family (8M–15B parameters) for sequence embedding, contact prediction, and structure prediction via ESMFold. Generates per-residue and per-sequence representatio

ESM-2/ESM-IF — Meta AI protein language models for embeddings, structure prediction, and inverse folding. ESM-2 provides learned representations (up to 15B parameters) for zero-shot variant effect pre

ESM-1v zero-shot variant-effect prediction for protein mutations from sequence. Use when users ask for ESM1v, mutation effect scoring, deep mutational scan labeling, or Meier et al. 2021 workflows wit

Use when predicting variant pathogenicity with EVE (Evolutionary model of Variant Effect) — an unsupervised deep generative model from the Marks Lab (OATML/Harvard) that scores missense variants using

Use when working with EvoAug -- a PyTorch library for evolution-inspired data augmentation of DNA sequences for training genomic deep learning models. EvoAug applies biologically motivated transforms:

Use when working with ExpansionHunter — Illumina's tool for genotyping short tandem repeats (STRs) and repeat expansions from PCR-free whole-genome sequencing data. Detects pathogenic repeat expansion

FarmCPU (Fixed and random model Circulating Probability Unification) — fast, powerful GWAS method for plant and agricultural genomics, implemented in the rMVP R package. Performs genome-wide associati

Use when performing Bayesian colocalization analysis between GWAS and eQTL data using fastENLOC (fast enrichment estimation-based co-localization). fastENLOC integrates eQTL probabilistic annotations

Use when mapping expression quantitative trait loci (eQTL), splicing QTL (sQTL), or protein QTL (pQTL) with FastQTL. Covers nominal pass, permutation pass, conditional analysis, beta-approximation FDR

Fiji/ImageJ — batteries-included distribution of ImageJ2 for scientific bioimage analysis. Batch macro scripting for cell counting, fluorescence quantification, and particle tracking. Bio-Formats supp

Fiji/ImageJ — open-source scientific image analysis platform for life sciences. Provides image segmentation, particle analysis, cell tracking, colocalization, 3D visualization, and batch processing of

Use when working with the rfishbase R package to query the FishBase database for fish species records, ecology, morphology, length-weight parameters, trophic levels, taxonomy, distribution, and reprod

FLAMES — Full-Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq data. R/Bioconductor pipeline for barcode demultiplexing, isoform discovery, transcript quantificatio

FlowSOM — high-performance self-organizing map (SOM) clustering for flow cytometry and mass cytometry (CyTOF) data. Build a SOM grid from multi-parameter single-cell marker expression, then apply cons

Use when performing TWAS fine-mapping or colocalization with FOCUS (Fine-mapping Of CaUsal Sets) or MA-FOCUS (Multiple Ancestry). Covers focus finemap, focus munge, focus import, posterior inclusion p

FoodMicrobionet routing skill for food microbiome network analysis, food microbial ecology, and co-occurrence network construction from 16S rRNA amplicon data. Use this skill when users mention FoodMi

Use this skill for FPSim2, the RDKit-based Python toolkit for high-throughput molecular fingerprint similarity search. Covers fingerprint database creation with fpsim2-create-db or create_db_file, in-

Funannotate is a eukaryotic genome annotation pipeline that integrates ab initio gene prediction, homology-based evidence, and functional annotation. Use when users ask about funannotate, eukaryotic g

FUNGuild — ecological guild annotation tool for fungal OTU/ASV tables from amplicon metagenomics. Assigns trophic modes (Saprotrophic, Pathotroph, Symbiotroph) and ecological guilds (Ectomycorrhizal,

GA4GH Beacon — federated genomic variant discovery API standard developed by the Global Alliance for Genomics and Health. Query whether a specific genomic variant (SNV, indel, CNV, structural variant)

GA4GH VRS (Variation Representation Specification) is a standard and Python library for representing biological sequence variants in a computable, interoperable form. Generates globally unique GA4GH V

Use this skill for GATK copy-number variation workflows including germline gCNV cohorts and somatic copy-ratio segmentation from WES or WGS data. Trigger on requests about CollectReadCounts, Determine

Use when working with GATK MarkDuplicates, Picard MarkDuplicates through the GATK wrapper, duplicate marking in BAM or CRAM files, duplicate metrics, or optical duplicate detection in short-read DNA s