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samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

sccatch_performance_comparison

The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database

scconsensus

An approach combining supervised and unsupervised clustering for cell type detection in single-cell RNA-seq data

scdeepcluster

scDeepCluster for Single Cell RNA-seq data

sceqtl

scikit-learn

scikit-learn: machine learning in Python

scina

SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples

scpolya-seq

https://pubmed.ncbi.nlm.nih.gov/36454750/

scrna-seq

scrna.seq.course

Analysis of single cell RNA-seq data course

scrnaseqpipeline

scsa

SCSA: cell type annotation for single-cell RNA-seq data

scte

security-on-github

seurat

R toolkit for single cell genomics

sincera

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

smartgpt

A nodejs implementation of AI Explained on youtube's SmartGPT prompting strategy for getting better responses from gpt4.

smartseq2

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

snakemakeworkflow

Bioinformatics-pipeline in snakemake.

snapatac

Analysis Pipeline for Single Cell ATAC-seq

snaphic

SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data

snpsplit

Allele-specific alignment sorting

sommer

sommer for Genomic Selection

souporcell

Clustering scRNAseq by genotypes

spsimseq

Semi-parametric simulation of bulk and single cell RNA-seq data

ssrge

statsmodels

Statsmodels: statistical modeling and econometrics in Python

survival

Survival package for R

systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool