Browse Tools

Use when performing single-cell QTL (sc-eQTL, sc-sQTL) mapping with SAIGE-QTL. SAIGE-QTL extends the SAIGE framework to single-cell RNA-seq data using Poisson mixed models to handle count overdispersi

Sailfish — rapid mapping-based isoform quantification from RNA-seq reads. Uses quasi-mapping to estimate transcript abundance without full alignment. Provides TPM and estimated counts per transcript.

Salmon is an ultrafast, bias-correcting tool for quantifying transcript abundances from RNA-seq reads using quasi-mapping or selective alignment. Alevin is Salmon's single-cell mode for generating cel

Sarek — nf-core Nextflow pipeline for germline and somatic variant calling from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing data. Supports multiple variant cal

scArches (Single-cell Architecture Surgery) — Python toolkit for reference-based single-cell data integration via transfer learning. Maps query datasets into pre-trained reference atlases using archit

scater — Bioconductor single-cell RNA-seq QC and visualization toolkit built on SingleCellExperiment. Use when user needs per-cell QC metrics with addPerCellQCMetrics, adaptive MAD-based outlier detec

scCODA — Bayesian compositional analysis for single-cell data using Dirichlet-multinomial models. Detects statistically credible changes in cell type compositions between conditions (e.g., disease vs

scDblFinder — Bioconductor R package for detecting doublets in single-cell RNA-seq data using simulation-based classification with gradient boosting. Identifies neotypic and heterotypic doublets in dr

SCENIC (pySCENIC) — gene regulatory network inference and transcription factor regulon analysis for single-cell RNA-seq data. Infers TF-target gene networks using GRNBoost2/GENIE3, refines regulons vi

scFoundation — large-scale pretrained foundation model for single-cell transcriptomics built on the xTrimo transformer architecture. Trained on ~50 million human single-cell profiles, scFoundation gen

scGPT — generative pretrained transformer foundation model for single-cell multi-omics analysis. Provides cell type annotation, gene perturbation prediction, multi-batch integration, multi-omic integr

scikit-image — Python library for image processing built on NumPy arrays. Provides filtering (gaussian, sobel, median, thresholding), segmentation (watershed, slic, felzenszwalb, random_walker), featu

sciPENN — neural network model for single-cell protein expression imputation and multi-omics integration. Transfers protein predictions from CITE-seq (paired RNA+protein) training data to unpaired RNA

scirpy -- Python toolkit for single-cell immune receptor (TCR and BCR) repertoire analysis built on the scverse ecosystem. Defines clonotypes from paired chain data using CDR3 nucleotide/amino acid se

Use when working with Scout — a web-based visualization and case management

Use when working with scran pooling normalization — scranpool — the pool-and-deconvolve size-factor estimation method for single-cell RNA-seq normalization. Pools cells to robustly estimate size facto

ScreenProcessing — Python pipeline for analyzing pooled genetic screens (CRISPRi/CRISPRa). Converts raw FASTQ sequencing files into library counts using fastqgz_to_counts.py, then generates sgRNA phen

scRepertoire -- R package for analyzing T cell receptor (TCR) and B cell receptor (BCR) repertoires from single-cell sequencing data. Integrates with Seurat and SingleCellExperiment objects to combine

scVelo — RNA velocity generalized through dynamical modeling. Estimates splicing kinetics from single-cell RNA-seq data using steady-state, stochastic, and dynamical models to infer cellular dynamics,

Seaborn — statistical data visualization library built on matplotlib. Provides high-level functions for relational plots (scatterplot, lineplot), distribution plots (histplot, kdeplot, ecdfplot), cate

Sentieon — commercial high-performance genomics toolkit implementing GATK-compatible algorithms (DNAscope, TNscope, Haplotyper, BQSR, Dedup) with 50x speed improvement over GATK. Provides germline SNV

Sequenza is a bioinformatics tool for allele-specific copy number analysis and tumor purity/ploidy estimation from tumor-normal paired sequencing data. It preprocesses BAM or pileup files into seqz fo

SeSAMe (SEnsible Step-wise Analysis of DNA MEthylation BeadChips) — R/Bioconductor package for processing Illumina Infinium DNA methylation arrays. Supports EPIC, EPICv2, HM450, HM27, MM285, and Mamma

SHAPEIT4/5 — statistical haplotype phasing for SNP array and whole-genome sequencing data. SHAPEIT5 is the current production version, providing phasing of common variants (MAF >= 0.1%) via phase_comm

ShortBRED — metagenomics protein-family quantification tool from the bioBakery suite. Identifies short, representative peptide markers from protein families and quantifies their relative abundance in

sigmap is a C++ tool for signal-level alignment of nanopore sequencing data, mapping raw electrical signals (squiggles) directly to a reference genome without basecalling. Uses Dynamic Time Warping (D

Signac — R toolkit for single-cell chromatin accessibility analysis built on Seurat. Processes scATAC-seq data from 10x Genomics and other platforms. Handles fragment files, performs TF-IDF normalizat

SigProfiler — Alexandrov Lab suite for somatic mutational signature analysis. Generates mutation matrices from VCF/MAF files (SigProfilerMatrixGenerator), extracts de novo mutational signatures via NM

SimpleITK — Python/multi-language interface to the Insight Toolkit (ITK) for medical image analysis. Supports image I/O (DICOM, NIfTI, MHA, MRC, NRRD, PNG/TIFF), image registration (rigid, affine, def

SIP (Significant Interaction Peak caller) — Java-based tool for identifying chromosomal loops (significant interaction peaks) in Hi-C contact maps. Processes .hic (Juicebox), .mcool (cooler), or pre-p

Skyline — free, open-source Windows application for building targeted mass spectrometry methods and quantitative analysis. Supports SRM/MRM, PRM, DIA (SWATH), and full-scan MS1 quantification with tra

Slingshot — R/Bioconductor package for trajectory inference in single-cell RNA-seq data. Infers branching lineage structures via cluster-based minimum spanning trees (MST), fits simultaneous principal

EIGENSOFT / smartpca — suite for population structure analysis and stratification correction in genome-wide genetic studies. smartpca performs principal component analysis (PCA) on genotype data to in

Snakemake — Python-based workflow management system for reproducible and scalable bioinformatics pipelines. Defines workflows as rules with inputs, outputs, and shell/script/wrapper directives connect

Use when working with SnapHiC — a computational method for identifying chromatin loops from single-cell Hi-C data. SnapHiC processes sparse single-cell contact maps, normalizes for distance decay and

snpStats is an R/Bioconductor package for GWAS (genome-wide association study) and population genetics analysis. It provides SnpMatrix and XSnpMatrix objects for efficient SNP data storage, PLINK bina

SoupX -- R package for estimating and removing ambient RNA contamination (soup) from droplet-based single-cell RNA-seq data. Works with 10x Chromium Cell Ranger output to estimate the contamination fr

Use when working with SparsePro for GWAS fine-mapping and causal variant identification. Sparse variational inference framework that computes posterior inclusion probabilities (PIPs) and credible sets

spatialdata is the scverse Python framework for managing, analyzing, and visualizing multi-modal spatial omics datasets. Provides a unified SpatialData object that stores images, segmentation labels,

SpatialDE -- Python package for identifying spatially variable genes in spatial transcriptomics data using Gaussian process regression. Tests whether gene expression exhibits spatial patterns beyond r

Spectronaut -- commercial DIA (Data-Independent Acquisition) proteomics software from Biognosys for analyzing DIA-MS data. Supports library-based and library-free (directDIA / Pulsar) peptide-centric

SpliceAI -- deep learning tool for predicting the impact of genetic variants on RNA splicing using raw DNA sequence context. Predicts four delta scores (acceptor gain, acceptor loss, donor gain, donor

SPOTlight — R/Bioconductor spatial transcriptomics deconvolution using seeded NMF regression. Estimates cell type proportions at each spatial location by integrating single-cell RNA-seq reference data

Squidpy — spatial single-cell analysis toolkit in the scverse ecosystem for analyzing and visualizing spatial molecular data. Builds spatial neighbor graphs from tissue coordinates (Visium, Xenium, ME

Stan — probabilistic programming language for Bayesian statistical modeling and high-performance inference. Full Bayesian inference via No-U-Turn Sampler (NUTS/HMC), approximate inference via Automati

STARmap (Spatially-resolved Transcript Amplicon Readout mapping) — in situ spatial transcriptomics method that combines hydrogel-tissue chemistry with sequencing-by-hybridization (SEDAL) for multiplex

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

Straglr — genome-wide detection and genotyping of tandem repeat (TR) expansions from long-read sequencing alignments (PacBio HiFi, ONT). Performs expansion scanning with configurable size thresholds a

STRING-db — protein-protein interaction (PPI) network database and API covering known and predicted interactions for over 67 million proteins across 14,000 organisms. Query functional protein associat

SummarizedExperiment — core Bioconductor container for rectangular genomics data matrices. Stores count matrices (assays) with row metadata (rowData, rowRanges for GRanges coordinates) and column meta