Browse Tools

Use when working with MultiXcan or S-MultiXcan — the multi-tissue extension of PrediXcan and S-PrediXcan for transcriptome-wide association studies (TWAS). Covers SMulTiXcan.py from the MetaXcan suite

Use when working with MungeSumstats — a Bioconductor R package for standardizing and quality-controlling GWAS (genome-wide association study) summary statistics. Covers the full MungeSumstats pipeline

Use when working with NanoCaller for SNP and short indel calling from long-read sequencing alignments (Oxford Nanopore and PacBio). NanoCaller combines haplotype-aware deep neural network SNP calling

NanoComp compares multiple Oxford Nanopore long-read sequencing datasets side-by-side, producing interactive HTML reports and TSV statistics across samples. Use when comparing read-length distribution

Napari — fast, interactive, multi-dimensional image viewer for Python built on Qt and vispy (OpenGL). Provides GPU-accelerated rendering of 2D, 3D, and nD image data with seven layer types (Image, Lab

NCBI/NIH tools — search, retrieve, and process biological data from NCBI databases (PubMed, GenBank, Gene, SRA, RefSeq, ClinVar, dbSNP, Taxonomy) using the NCBI E-utilities REST API and NCBI Datasets

needletail — high-performance Rust-based FASTA/FASTQ parser with Python bindings. Parse FASTA and FASTQ files at near-C speed using parse_fastx_file and parse_fastx_string. Provides k-mer extraction w

netneurotools (NetNeuroTools) for network neuroscience workflows: dataset fetchers for canonical brain templates and atlases, graph construction and consensus network methods, modularity consensus clu

NetPyNE — Python interface for multi-scale biological neural network simulation built on NEURON. Specify network populations, multi-compartment cell models, synaptic connections, plasticity rules, and

neuromaps — Python toolbox for registration, transformation, and statistical comparison of brain annotation maps across standard neuroimaging coordinate spaces (MNI152, fsaverage, fsLR, CIVET). Fetche

Use when working with NeuronJ — an ImageJ/Fiji plugin for semi-automatic tracing and quantification of elongated image structures such as neurons, axons, dendrites, and neurites in microscopy images.

nf-core/chipseq — Nextflow pipeline for comprehensive ChIP-seq analysis from raw reads through peak calling and differential analysis. Automates adapter trimming, multi-aligner support (BWA, Bowtie2,

Use when working with nf-core/differentialabundance — a reproducible Nextflow pipeline for differential abundance analysis of count data from RNA-seq, ATAC- seq, proteomics, or any feature-by-sample c

Use when working with nf-core/hic — a reproducible Nextflow pipeline for Hi-C and related proximity ligation sequencing (Micro-C, DNase Hi-C, in-situ Hi-C) data analysis. Processes paired-end FASTQs t

nf-core/methylseq — community-curated Nextflow pipeline for whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data analysis. Handles adapter trimming (Tri

Use when working with nf-core/nanoseq — a reproducible Nextflow pipeline for Oxford Nanopore Technology (ONT) long-read sequencing data. Covers basecalling (Guppy/Dorado), alignment (minimap2), QC (Na

Use when working with nf-core/rnafusion — a reproducible Nextflow DSL2 pipeline for RNA fusion gene detection from RNA-seq data. Detects gene fusions using multiple callers: STAR-Fusion, Arriba, Fusio

nf-core/rnaseq — production Nextflow pipeline for bulk RNA-seq analysis including read QC, trimming, alignment (STAR/HISAT2), pseudo-alignment (Salmon), quantification, and comprehensive quality contr

nf-core/scrnaseq — Nextflow pipeline for single-cell RNA-seq quantification and preprocessing. Supports multiple alignment/quantification methods including Cell Ranger, STARsolo, Alevin-fry (Salmon),

nf-core/viralrecon — Nextflow pipeline for viral genome reconstruction and analysis from sequencing data. Supports Illumina and Oxford Nanopore reads for SARS-CoV-2, influenza, and other viral genomes

ngs.plot — fast R-based visualization tool for next-generation sequencing data enrichment at functional genomic regions. Generates average profiles and heatmaps from BAM files over TSS, TES, gene bodi

Niche identifies cellular microenvironments and spatial niches in spatial transcriptomics data. Construct spatial neighborhood graphs, compute niche-level gene expression profiles, cluster cells by ni

NIMBLE — R package for hierarchical statistical modeling using MCMC, particle filtering, Laplace approximation, and programmable algorithms. Extends the BUGS/JAGS language with customizable samplers,

Use when performing differential expression analysis on RNA-seq count data using NOISeq or NOISeqBIO. Covers the full workflow: data object creation with readData, quality control with dat and explo.p

Oases — de novo transcriptome assembler for short-read RNA-seq data built on the Velvet de Bruijn graph framework. Performs transcript assembly across varying expression levels using multi-k-mer merge

OceanParcels (Parcels) is a Python framework for Lagrangian ocean analysis: it tracks virtual particles through 2D/3D hydrodynamic velocity fields from ocean models or observational products. Use this

Use when working with OneK1K tools from the Powell Genomics Lab — the single-cell eQTL (sc-eQTL) analysis suite built around the OneK1K cohort (~1.27 million PBMCs from 982 donors). Covers the full pi

Oxford Nanopore Technologies (ONT) sequencing data analysis skill. Covers the end-to-end nanopore pipeline: basecalling raw POD5/FAST5 signal with Dorado, long-read alignment with Minimap2, haploid co

OpenFold — open-source PyTorch reimplementation of AlphaFold2 for trainable protein structure prediction. Supports custom training on user datasets, fine-tuning of structure prediction models, and inf

Orcasound: open-source bioacoustics platform for real-time hydrophone audio streaming, orca (killer whale) call detection, and acoustic ML model training. Process underwater audio streams, generate sp

Use when identifying, quantifying, or analyzing Open Reading Frames (ORFs) from Ribo-seq, RNA-seq, or genomic sequences using ORFik — a comprehensive R/Bioconductor toolkit for translation analysis. C

org.Hs.eg.db is the Bioconductor OrgDb package for genome-wide human gene annotation built primarily around Entrez Gene identifiers. Use this skill when users need human gene ID conversion, symbol loo

Use when working with org.Mm.eg.db, mouse genome annotation, Mus musculus gene annotation in R, or Bioconductor AnnotationDbi lookups for mouse. The org.Mm.eg.db package provides genome-wide annotatio

outbreak.info is a unified COVID-19 and SARS-CoV-2 data platform with three main surfaces: authenticated genomics endpoints for lineage and mutation prevalence, public epidemiology endpoints for cases

Computational paleontology skill for non-DNA analysis of fossil data. Covers geometric morphometrics (landmark-based shape analysis with geomorph), diversity dynamics (extinction and origination rates

Use when working with pandas — the foundational Python data analysis library — for tabular data manipulation, CSV/TSV/Excel/HDF5/Parquet I/O, DataFrame operations, and bioinformatics data wrangling. p

Use when working with pathview, the R/Bioconductor package for KEGG pathway-based data integration and visualization. Covers overlaying gene expression data (fold changes, p-values, counts) onto KEGG

PathVisio biological pathway editor and analysis tool. Draw and edit biological pathways in GPML (Graphical Pathway Markup Language) format. Load gene expression or metabolomics data onto pathways for

PCAdapt is a CRAN/Bioconductor R package for genome scans to detect local adaptation in population genomics. Uses PCA-based Mahalanobis distance to identify outlier SNPs under selection without requir

PCAWG (Pan-Cancer Analysis of Whole Genomes) pipelines — standardized bioinformatics workflows from the ICGC-TCGA Pan-Cancer consortium for whole-genome somatic analysis of cancer samples. Includes al

Peakachu is a machine-learning tool for calling chromatin loops from Hi-C and Micro-C contact maps. Uses random forest classifiers trained on ChIA-PET, HiChIP, or CTCF ChIP-seq loop anchors to predict

PEER (Probabilistic Estimation of Expression Residuals) is a Bayesian sparse factor analysis framework for inferring and removing hidden confounders from gene expression data before eQTL, sQTL, and pQ

PEPPER (Position Encoding with Positional Encoding Representations) — a recurrent neural network (RNN)-based variant discovery tool for Oxford Nanopore (ONT) long-read sequencing data. PEPPER generate

PEPPER-Margin-DeepVariant — end-to-end haplotype-aware variant calling pipeline for long-read sequencing data (Oxford Nanopore Technology and PacBio HiFi). Combines PEPPER (RNN-based candidate variant

Perseus — computational platform for comprehensive statistical analysis of quantitative proteomics data. Companion to MaxQuant, Perseus provides an interactive workflow environment for processing prot

Use when working with pertpy, the scverse framework for single-cell perturbation analysis in Python. Trigger this skill for Perturb-seq, CRISPR screen QC, perturbation signatures, Mixscape, Milo, Augu

PGS Catalog tools — Python utilities and Nextflow pipeline for downloading, matching, calculating, and validating polygenic scores (PGS) from the EMBL-EBI PGS Catalog (pgscatalog.org). Provides pgscat

Use when working with PhaBOX2 PhaMer virus identification on assembled viral or phage contigs. This skill routes users to the documented `phabox2 --task phamer` workflow, including FASTA input prepara

PHASTER (PHAge Search Tool Enhanced Release) is a web server and REST API for rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Accepts NCBI accession nu

Phytozome utilities — search, browse, and download plant genome assemblies, gene annotations, protein sequences, and comparative genomics data from the JGI Phytozome plant genomics portal. Supports qu