Browse Tools

Use when working with piano, Platform for integrative analysis of omics data, directional gene set analysis in R, or Bioconductor workflows built around runGSA, loadGSC, GSAsummaryTable, consensusScor

Use when classifying plant protein sequences into gene families, estimating gene family evolution, or performing phylogenomic analysis with PlantTribes2. Covers scaffold-based gene family classificati

PlasmoDB is the VEuPathDB genomic resource for Plasmodium and Apicomplexa parasites (Toxoplasma, Cryptosporidium, Babesia, Eimeria, and others). Query gene annotations, expression data, ortholog group

PlasmoDB — the Plasmodium genome resource and functional genomics database for malaria parasites. Part of VEuPathDB, it provides genomic, transcriptomic, and proteomic data for Plasmodium species incl

Plass is a protein-level assembler for short-read metagenomic and metatranscriptomic datasets. Route to this skill when users ask for `plass`, protein-level assembly, metagenome ORF assembly, or Pengu

Polars — high-performance DataFrame library written in Rust with Python and Rust APIs. Built for speed, parallelism, and out-of-core processing via lazy evaluation and SIMD acceleration. Use for: fast

Poly is a Go library and CLI for engineering biological sequences. Core capabilities: read/write GenBank, FASTA, GFF, SnapGene, SBOL, and FASTQ formats; codon optimization for heterologous expression;

Popcorn — cross-population heritability and genetic architecture estimation from GWAS summary statistics. Computes population-specific and cross-population LD scores from reference panels, then fits a

poppr — R/CRAN package for genetic analysis of populations with clonal or partially clonal reproduction. Computes multilocus genotype (MLG) diversity, clone correction, index of association (IA) for l

PrediXcan/MetaXcan — Python suite for transcriptome-wide association studies (TWAS) using individual-level genotype data (PrediXcan) or GWAS summary statistics (S-PrediXcan, S-MultiXcan). Predicts tis

PRIDE tools are EMBL-EBI proteomics data repository utilities for submitting, querying, and downloading mass spectrometry datasets from the PRIDE Archive. Use this skill for ProteomeXchange dataset su

PROGENy (Pathway RespOnsive GENes) is an R/Bioconductor package and Python decoupler-py model for inferring the activity of 14 cancer-relevant signaling pathways (EGFR, MAPK, PI3K, JAK-STAT, TGFb, TNF

Use when working with ProtTrans — a family of protein language models (ProtT5, ProtBert, ProtAlbert, ProtXLNet, ProtElectra) — for generating protein sequence embeddings, secondary structure predictio

Use when working with pyclesperanto or pyclesperanto_prototype, the OpenCL- accelerated GPU image processing library for Python. Covers GPU-accelerated 2D/3D image filtering (Gaussian blur, top-hat, D

PyVista — Python 3D visualization and mesh analysis library built on VTK. Creates interactive and publication-quality 3D renderings of meshes, point clouds, structured and unstructured grids, and volu

QTLtools — complete tool chain for molecular QTL discovery and analysis. Run cis-QTL mapping (nominal, permutation, conditional passes), trans-QTL mapping, and multi-phenotype analysis for eQTL, sQTL,

quantms — Nextflow pipeline for quantitative proteomics mass spectrometry. Supports DDA (Data-Dependent Acquisition) and DIA (Data-Independent Acquisition) workflows with label-free, TMT, and iTRAQ la

RagTag — reference-guided genome scaffolding, assembly correction, and gap patching for draft genome assemblies. Use ragtag scaffold to order and orient contigs using a reference genome, ragtag correc

spacexr (RCTD) — R package for Robust Cell Type Decomposition of spatial transcriptomics data. Deconvolves cell type mixtures in spatial spots using single-cell RNA-seq references. Supports three mode

Use when working with ReactomeFIViz — a Cytoscape 3 app for Reactome Functional Interaction (FI) network analysis. Visualizes and analyzes the Reactome FI network (~300k functional interactions among

Computational tools and workflows for regenerative medicine research: stem cell differentiation trajectory analysis, iPSC quality control, cell therapy manufacturing analytics, organoid single-cell pr

Use when working with rentrez, the rOpenSci R package for the NCBI Entrez E-utilities API. Covers entrez_search, entrez_fetch, entrez_summary, entrez_link, entrez_post, entrez_info, entrez_dbs, entrez

Use when integrating R and Python with reticulate: importing Python modules from R, declaring Python dependencies with py_require(), selecting Python environments (use_python/use_virtualenv/use_condae

Use when working with ribosome profiling (Ribo-seq) data to perform P-site offset estimation, quality control, and occupancy analysis using RiboWaltz — an R/Bioconductor package for comprehensive ribo

Use when working with Rsubread, the Bioconductor R package for read alignment, exon junction discovery, feature counting, long-read mapping, annotation flattening, and alignment QC. Covers buildindex(

rust-bio — high-performance Rust library for bioinformatics algorithms

rust-htslib — safe Rust bindings to htslib for reading and writing BAM, SAM, CRAM, VCF, BCF, tabix, BGZF, and FASTA index files. Provides bam::Reader, bam::IndexedReader, bcf::Reader, bcf::Writer, fai

rvtests — Rare Variant Tests: a C++ command-line toolkit for genome-wide association studies (GWAS) with a focus on rare-variant burden, collapsing, and sequence-kernel association tests (SKAT, SKAT-O

S-LDSC (stratified LD score regression) partitions SNP heritability across functional annotations and cell types from GWAS summary statistics. Use for heritability enrichment analysis, cell-type-speci

Use when working with S-PrediXcan from the MetaXcan suite to compute transcriptome-wide association statistics from GWAS summary data and PredictDB model databases. Covers GWAS column mapping, allele

Use when working with SAMap for cross-species single-cell RNA-seq atlas alignment, manifold mapping, homolog graph construction, or cell-type conservation analysis. SAMap maps AnnData or SAM objects a

Use when calculating sample size for two-sample and paired t-tests, Wilcoxon-Mann-Whitney tests on ordered categorical outcomes with ties, or Cochran-Mantel-Haenszel mean-score trend tests with the R

Use when working with SATURN for cross-species single-cell RNA-seq integration that combines AnnData count matrices with protein embedding TorchDicts. SATURN trains macrogene representations with k-me

Use when working with SAVANA, long-read somatic structural variant calling, tumour-normal cancer BAM analysis, tumour-only SV calling, or integrated copy number analysis (SCNA) from long-read sequenci

SBML tools skill for Systems Biology Markup Language model validation, inspection, conversion, and reproducible preprocessing using libSBML. Use this when users ask about SBML Level/Version compatibil

scanpy-plots — visualization layer of the Scanpy single-cell RNA-seq analysis suite (scanpy.pl module). Generates UMAP, t-SNE, PCA embeddings, violin plots, dot plots, heatmaps, matrix plots, stacked

scBERT is a transformer-based single-cell RNA-seq annotation workflow from Tencent AI Lab Healthcare that follows a pretrain-and-fine-tune pattern for cell type labeling. Use this skill when users men

Use when working with scCustomize — an R package providing enhanced, publication-quality visualization functions for single-cell RNA-seq data. Extends Seurat and ggplot2 with clustered dot plots, stac

scDALI — differential allelic imbalance and allele-specific expression (ASE) analysis in single-cell RNA-seq data using Gaussian process models. Detects whether allelic imbalance changes along cell st

scde is a Bioconductor R package for Bayesian single-cell differential expression analysis using mixture models. It fits a per-cell error model (negative binomial + Poisson noise) to raw count data, t

scHPF — single-cell Hierarchical Poisson Factorization for de novo gene program discovery in scRNA-seq data. Decomposes raw UMI count matrices into interpretable cell scores (theta) and gene loadings

scikit-learn — open-source Python machine learning library providing consistent estimator API for classification, regression, clustering, dimensionality reduction, model selection, and preprocessing.

scimap — Python toolkit for multiplexed imaging spatial single-cell analysis (CODEX, CyCIF, IMC, MIBI, mIHC). Loads MCMICRO quantification CSV outputs into AnnData, performs marker-based hierarchical

Use when working with scMoMaT, single-cell mosaic integration, multi-omics matrix tri-factorization, or marker discovery across RNA, ATAC, and protein batches with missing modalities. scMoMaT integrat

Use this skill for SCpubr workflows producing publication-quality visualizations of single-cell RNA-seq data in R. Covers UMAP/dimensionality reduction plots, violin plots, feature plots, dot plots, h

Use this skill for SCTransform normalization of single-cell RNA-seq count matrices. Route here when users ask about variance stabilizing transformation (VST), regularized negative binomial regression

scverse — the community-maintained Python ecosystem for single-cell and spatial omics analysis. Coordinates AnnData (universal data structure), scanpy (scRNA-seq QC/clustering/DE), squidpy (spatial tr

Use when working with Sei — the FunctionLab sequence-to-activity deep learning framework for predicting chromatin profiles and regulatory activity from DNA sequences. Sei takes 4096 bp DNA windows and

sequoia — R package for pedigree reconstruction and parentage assignment in animal, veterinary, and zoological genomics. Reconstructs multi-generational pedigrees from SNP genotype data combined with

Use when working with ShortRead, the Bioconductor package for FASTQ and FASTA quality control, chunked read iteration, random sampling, filtering, trimming, and QA reporting in R. Covers FastqStreamer