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sigma-1

Mutational signature analysis for low statistics SNV data

sigmajs

Σ sigma.js for R

sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R

signature.tools.lib

R package containing useful functions for mutational signature analysis

signatureanalyzer-gpu

SignatureAnalyzer-GPU provides a Tensorflow implementation of automatic relevance determination non-negative matrix factorization (ARD NMF).

signit

Mutation Signatures in Individual Tumours Deciphered by MCMC

sigprofilerclusters

Revised version of SigProfilerClusters

sigprofilerextractor

SigProfilerExtractor

sigprofilermatrixgenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

sigprofilerplotting

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

sigprofilerplottingr

An R wrapper for running the SigProfilerPlotting framework

simple-r

Automatically exported from code.google.com/p/simple-r

simseq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

single-cell-bioinformatics-scrm-2016

Single cell bioinformatics class at the Sanford Consortium for Regenerative Medicine (SCRM) in 2016

single-cell-erna

tool for finding enhancer rnas in single cell rna seq data

singlecellseq

singularity-tutorial

Materials for 3 hour hands-on workshop entitled "Creating and running software containers with Singularity"

sj2psi

Convert RNA-STAR aligner "SJ.out.tab" files to "Percent spliced-in" (Psi) scores

skidb

Reference data utilities for mskilab

skimr

A frictionless, pipeable approach to dealing with summary statistics

skymap

sleuth

Inspect kallisto RNA-Seq output

slope-spam

smc-het-challenge-examples

Galaxy tool integration examples for the SMC Het Challenge

snakechunks

Modular blocks to build Snakemake workflows for reproducible NGS analyses

snakewrappers

Snakemake wrappers, specifically designed for the NIH Biowulf system using TACC Modules

snowman

Structural variation and indel detection using rolling local string graph assembly

snprelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development Version)

soapdenovo-trans

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

solarplot

Mitochondrial Solar Plot