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scrna_10x

scrna_smart_seq2

scrublet

Detect doublets in single-cell RNA-seq data

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

seq2hla

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

seqtk

Toolkit for processing sequences in FASTA/Q formats

seurat

R toolkit for single cell genomics

shainmutectfilter

Shain Lab UCSF Post Mutect2 Filters

shiny-iatlas

An interactive web portal for exploring immuno-oncology data

sigminer

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

simplifygo

Simplify GO enrichment results

single-cell-metabolic-landscape

Pipeline for exploring metebolic heterogeneity at single-cell resolution

single-t-cell-data-access

Here we provide the DATA ACCESS AGREEMENT for single T cell data which deposited in the European Genome-phenome Archive with the access number EGAS00001002791

single_cell_classification

Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles

single_cell_lung_adenocarcinoma

singlecell-multiomics

singlecellnet

SingleCellNet: classify single cells across species and platforms

singleseqgset

Gene set enrichment analysis for single-cell RNAseq data

slicer

Multi-platform, free open source software for visualization and image computing.

slicerjupyter

Extension for 3D Slicer that allows the application to be used from Jupyter notebook

smoothhr

:exclamation: This is a read-only mirror of the CRAN R package repository. smoothHR — Smooth Hazard Ratio Curves Taking a Reference Value

snapatac

Single Nucleus Analysis Package for ATAC-seq

souporcell

Clustering scRNAseq by genotypes

soupx

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

sourcetracker2

SourceTracker2

spatil

A strategy to quantify the spatial arrangement of the tumor microenvionment

spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs

sprint

SNP-free RNA editing Identification Toolkit

squire

Software for Quantifying Interspersed Repeat Expression