Purdue University

Sage is a proteomics search engine - a tool that transforms raw mass spectra from proteomics experiments into peptide identificatons via database searching & spectral matching. But, it's also more than just a search engine - Sage includes a variety of advanced features that make it a one-stop shop: retention time prediction, quantification (both isobaric & LFQ), peptide-spectrum match rescoring, and FDR control.

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.

Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files.

Samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.

Samclip is a tool to filter SAM file for soft and hard clipped alignments.

Samplot is a command line tool for rapid, multi-sample structural variant visualization.

Samtools is a set of utilities for the Sequence Alignment/Map (SAM) format.

SAS is a commercial integrated system for statistical analysis, data mining, and graphics as well as many enterprise oriented additional features.

ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. It depends on external libraries including BLAS and LAPACK for Linear Algebra computations.

Scanpy is scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

scArches is a package to integrate newly produced single-cell datasets into integrated reference atlases.

scGen is a generative model to predict single-cell perturbation response across cell types, studies and species.

Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.

scVelo is a scalable toolkit for RNA velocity analysis in single cells

scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at UC Berkeley.

Segalign is a scalable GPU system for pairwise whole genome alignments based on LASTZ's seed-filter-extend paradigm.

Seidr is a community gene network inference and exploration toolkit.

Sentaurus is a suite of TCAD tools which simulates the fabrication, operation and reliability of semiconductor devices. The Sentaurus simulators use physical models to represent the wafer fabrication steps and device operation, thereby allowing the exploration and optimization of new semiconductor devices.

Sepp stands for SATé-Enabled Phylogenetic Placement and addresses the problem of phylogenetic placement for meta-genomic short reads.

SeqCode is a family of applications designed to develop high-quality images and perform genome-wide calculations from high-throughput sequencing experiments. This software is presented into two distinct modes: web tools and command line.