Browse Tools

Use when performing rare variant association tests with SKAT, SKAT-O, or burden tests. SKAT (Sequence Kernel Association Test) is an R package for gene-based and region-based rare variant association

Use when performing rare variant association testing with SKAT-O (Sequence Kernel Association Test - Optimal). Optimal unified test combining SKAT and burden tests for SNP-set or gene-based analysis.

SlideGraph+ — graph-based deep learning framework for whole slide image (WSI) analysis in computational digital pathology. Builds spatial and hierarchical graphs from WSI patch features, then trains g

SLiM (Selection on Linked Mutations) is a forward-time, individual-based population genetics simulator with the Eidos scripting language. Use when users need to simulate natural selection, genetic dri

SMR/HEIDI — Summary-data-based Mendelian Randomization with HEIDI test for colocalization and causal inference between eQTL summary data and GWAS traits. Identifies genes whose expression levels are c

Use when working with SnapGene Viewer, the free desktop application for visualizing plasmid maps, DNA sequences, and genomic features in molecular biology. Covers reading and converting .dna files (Sn

Use when working with SNF, SNFtool, or Similarity Network Fusion for multi-omics integration, patient subtyping, fused similarity networks, or multi-view clustering in R. SNFtool accepts feature matri

Space Ranger is 10x Genomics software for processing Visium spatial gene expression and HD Visium datasets. Use this skill when users need to run `spaceranger count`, aggregate multiple runs with `spa

Use when working with SpaGCN for spatial transcriptomics domain detection, histology-aware adjacency construction, graph-convolution clustering, spatially variable gene (SVG) discovery, or meta-gene i

ST Pipeline — automated processing pipeline for spatial transcriptomics (Spatial Transcriptomics method). Handles demultiplexing, quality trimming, contamination filtering, genome alignment, annotatio

Spectra routing skill for mass spectrometry data representation and manipulation in R/Bioconductor. Use this skill when users mention Spectra, RforMassSpectrometry, MsBackend, MsBackendMzR, MsBackendH

Spectre is an R toolkit for high-dimensional single-cell cytometry and imaging analysis, including data import (CSV/FCS), metadata integration, arcsinh/logicle transformation, clustering (FlowSOM, Phe

Use this skill for SpiecEasi — sparse inverse covariance estimation for ecological association inference in microbiome studies. Route here when users ask about SPIEC-EASI, microbial co-occurrence netw

Splatter is an R/Bioconductor package for simulating single-cell RNA-seq (scRNA-seq) count data. Use when users need to generate synthetic scRNA-seq datasets for benchmarking clustering, trajectory, o

SPM12 (Statistical Parametric Mapping 12) — the standard neuroimaging analysis framework for fMRI, PET, VBM, and EEG/MEG data. Use for preprocessing (realignment, slice-timing, normalisation, smoothin

squidpy plots — sq.pl visualization module for spatial omics data. Generates publication-ready spatial scatter plots with cell-type or gene-expression overlays, neighborhood enrichment heatmaps, co-oc

Use when working with STAAR — Sequence Kernel Association Test Accounting for Relatedness. R package for rare-variant association analysis of whole-genome sequencing (WGS) data. Supports BURDEN, SKAT,

Use when working with STAARpipeline for biobank-scale whole-genome or whole-exome rare-variant association analysis in R. Covers aGDS preparation, null model fitting, single-variant tests, gene-centri

Use when working with stageR, the Bioconductor R package for stage-wise testing in RNA-seq transcriptomics. Covers two-stage testing workflows for differential expression (DESeq2/edgeR/limma-voom) and

StarDist — deep learning framework for cell and nuclei detection and instance segmentation in 2D and 3D microscopy images using star-convex polygons. Predicts radial distances to object boundaries alo

STARsolo — ultrafast single-cell RNA-seq alignment, barcode processing, and UMI counting. STARsolo is a high-performance alternative to Cell Ranger for processing droplet-based (10x Genomics, Drop-seq

STELLAR (Spatial TEmporal Learning of cell-type cLAssification on multiple Regions) — graph neural network method for automated cell-type annotation in multiplexed imaging data. Transfers cell-type la

Use when working with StellarPGx, the Nextflow pipeline for calling star alleles in highly polymorphic pharmacogenes using genome graph-based variant detection. Covers CYP2D6, CYP2A6, CYP2B6, CYP2C19,

sumstatcolumns — GWAS summary statistics column harmonization utility from Nealelab's sumstat_utils. Standardizes, renames, filters, and validates column headers across summary statistics formats (BOL

surfplot — Python library for publication-quality cortical surface visualization in neuroimaging. Creates brain surface plots from GIFTI, CIfTI, or numpy array data overlaid on standard surfaces (fsLR

SuSiE-inf — Bayesian fine-mapping with an infinitely large number of effects. Python implementation extending SuSiE to handle highly polygenic regions by placing a spike-and-slab prior on infinitely m

Use when working with susieR (Sum of Single Effects in R) for Bayesian fine-mapping of genetic associations. Covers individual-level genotype fine-mapping with susie(), summary-statistics fine-mapping

SymSim is an R package for simulating single-cell RNA sequencing (scRNA-seq) data using a mechanistic two-stage kinetic model. Use when users need to generate realistic synthetic scRNA-seq datasets wi

SynVisio is a web-based interactive tool for visualizing plant genome synteny blocks. Takes collinearity files from MCScan/MCScanX and genome annotation files (GFF/BED) to produce dot plots, synteny b

table2asn is the NCBI command-line tool for converting FASTA sequences and feature tables into ASN.1 (.sqn) files for submission to GenBank, RefSeq, and related NCBI databases. Handles prokaryotic and

TAIR (The Arabidopsis Information Resource) — the primary genomic database for Arabidopsis thaliana, providing gene models, functional annotations, protein sequences, metabolic pathways (AraCyc), stoc

Tangram — deep learning framework for mapping single-cell and single-nucleus gene expression data onto spatial transcriptomics data. Built on PyTorch and scanpy, Tangram optimizes a probabilistic mapp

TargetScan predicts biological targets of miRNAs in vertebrates by searching 3'UTR sequences for conserved matches to the miRNA seed region (8mer, 7mer-m8, 7mer-A1, 6mer sites). Computes context++ sco

Use when working with tascCODA for tree-aggregated compositional analysis of high-throughput sequencing data, especially single-cell RNA-seq, microbiome, or amplicon count tables with a lineage or tax

Tax4Fun2 is an R package for predicting the functional capabilities of prokaryotic communities based on 16S rRNA gene sequencing data. It allows for the functional annotation of amplicon sequence vari

TensorFlow — open-source machine learning framework for building and deploying deep learning models. Provides Keras high-level API for model building, tf.data for input pipelines, tf.image for image p

TeselaGen — integrated synthetic biology platform for DNA sequence design, combinatorial library construction, lab automation, NGS analysis, and ML-guided protein engineering. Modules: DESIGN (sequenc

TEtools is a Docker container suite maintained by the Dfam consortium that bundles RepeatMasker, RepeatModeler2, and complementary tools for transposable element (TE) annotation, repeat library constr

Use when working with TIAToolbox (TIA Toolbox) for computational pathology, whole-slide imaging, stain processing, patch extraction, and model inference. Covers documented TIAToolbox CLI workflows inc

Use when working with tidybulk, the Bioconductor R package that brings transcriptomics into tidyverse-style pipelines. Covers SummarizedExperiment-aware workflows for identify_abundant, keep_abundant,

Use when working with tidySingleCellExperiment, the R/Bioconductor adapter that makes SingleCellExperiment objects behave like tidy tibbles while preserving compatibility with the Bioconductor single-

TMHMM predicts transmembrane helices in protein sequences using a hidden Markov model. Use when users ask for transmembrane topology prediction, TM helix counting, inside/outside orientation assignmen

Use when working with topGO, the Bioconductor package for Gene Ontology enrichment analysis that accounts for the GO graph topology. Covers `topGOdata` object construction, `annFUN.org`, `annFUN.gene2

Use this skill for TotalSegmentator, the deep-learning tool for robust segmentation of 104-117 anatomical structures from CT (and MRI) images. Covers CLI usage (`TotalSegmentator -i ct.nii.gz -o seg/`

ToxoDB — integrated genomic and functional database for Toxoplasma gondii and related apicomplexan parasites within the VEuPathDB ecosystem. Provides gene search, BLAST, genome browser (GBrowse/JBrows

trackViewer is an R/Bioconductor package for visualizing multi-omics data as tracks or lollipop plots. It facilitates integrated analysis of NGS data such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNP

treeio — Bioconductor R package for importing and exporting phylogenetic tree data with associated metadata. Reads and writes Newick, Nexus, BEAST, RAxML, FastTree, IQ-TREE, MrBayes, PHYLODOG, r8s, ME