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single_cell_intestine

R code for single-cell analysis of intestinal epithelial cells

single_cell_portal

单细胞数据库Tutorials, workflows, and convenience scripts for Single Cell Portal

singlecell_endodiff_paper

单细胞关于SNP文章相应的脚本Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

singler0.2.2

SingleR: Single-cell RNA-seq cell types Recognition

singleseqgset

单细胞基因集富集Gene set enrichment analysis for single-cell RNAseq data

slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

smart-seq3

全长转录本单细胞smart-seq3Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).

snare_prep

同时测单细胞转录组和单细胞ATAC数据dropseq-based single nuclei genomic accessibility and RNA expression (SNARE-seq) preprocessing pipeline

sniffles

检测长片段的结构变异Structural variation caller using third generation sequencing

snpsea

:bar_chart: Identify cell types and pathways affected by genetic risk loci.

sonar

抗体分析Software for Ontogenic aNalysis of Antibody Repertoires

souporcell

10xGenomics单细胞转录组snp聚类Clustering scRNAseq by genotypes

soupx

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

spatialanalysisworkflows

speed2

SPEED2:Inferring upstream pathway activity from differential gene expression

spotlight

空间转录组与单细胞转录组整合-每个splots的细胞类型比例Spatial Transcriptomics Capture Location Deconvolution

spring_dev

一种用于单细胞数据交互探测的工具

sscclust

张泽明实验用于单细胞分析的pipelinesimpler single cell RNAseq data clustering

st-mliver

小鼠肝脏空间转录组Code associated with the manuscript Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver

starbase

DEPRECATED - HBase Stargate (REST API) client wrapper for Python.

stream

2019年发布的文献关于拟时间分析的方法STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

sttkit

空间转录组Pipeline for SpatialTranscriptomics and 10X Visium data

stutility

空间转录组多样品合并

svviz

结构变异可视化Read visualizer for structural variants

syngeneic_scrnaseq

2018年癌症单细胞细胞通讯特征代码 Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

tagfinder

DEL库--efficient DEL results analysis

tanaylab.github.io

单细胞转录组转座子

targetseqview

Visualize next generation sequencing reads over putative structural variants

tbsp

基于SNP和基因表达的拟时间分析，在monocle2的基础上再做拟时间分析Trajectory Inference Based on SNP information.

tcr-dist

VDJ分析流程，与10xvdj兼容Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)