# scRNA-codes

**Repository Path**: biojian/scRNA-codes

## Basic Information

- **Project Name**: scRNA-codes
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2026-05-19
- **Last Updated**: 2026-05-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# scRNA-codes Materials

> Author: Reed Liu
> This is my first single cell practice.
> **All the PDFs can be directly read!**

I will share my learning process of 10X and Smart-seq2 to fans of **Bioinfoplanet(公众号：生信星球)**.

### My Understanding_个人整理

#### Review_综述

- [单细胞转录组分析综述](https://github.com/reedliu/scRNA-codes/blob/master/my_understanding/%E5%8D%95%E7%BB%86%E8%83%9E%E8%BD%AC%E5%BD%95%E7%BB%84%E9%89%B4%E5%AE%9A%E7%BB%86%E8%83%9E%E7%BE%A4%E4%BD%93.md)：[2017-Identifying_cell_populations_with_scRNASeq.pdf](https://github.com/reedliu/scRNA-codes/blob/master/scRNA-papers/2017-Identifying_cell_populations_with_scRNASeq.pdf) 

#### Scripts_常用脚本

- [cellranger count操作](https://github.com/reedliu/scRNA-codes/tree/master/cellranger) 
- [校正批次效应](https://github.com/reedliu/scRNA-codes/blob/master/19.6.23-scRNA-batch-effect/three-scRNA-batch.R)
- [seurat V3操作（以PBMC 2700为例）](https://github.com/reedliu/scRNA-codes/blob/master/2019-07-scRNA-PBMC2700/seurat-v3-pbmc3k.R) 
- [seurat组合10X数据](https://github.com/reedliu/scRNA-codes/blob/master/seurat-combine-two-10X-runs.R) 
- [monocle2使用](https://github.com/reedliu/scRNA-codes/blob/master/monocle2_use_scRNA_pkg.R)
- [monocle3使用](https://github.com/reedliu/scRNA-codes/blob/master/monocle3-learn.R) 
- [用几个R包寻找HVGs](https://github.com/reedliu/scRNA-codes/blob/master/scRNA-HVGs-testing.R)
- [Bioconductor-scRNA之基础操作 ](https://github.com/reedliu/scRNA-codes/blob/master/bioconductor-scRNA-basic/part2_read_count_data.R) 
- [mouce_c1下游分析全套](https://github.com/reedliu/scRNA-codes/tree/master/2019-10-23-mouse_c1_downstream) 
- [改造Seurat的DoHeatmap函数](https://github.com/reedliu/scRNA-codes/blob/master/change_Seurat_DoHeatmap.R) 【配套说明：[如何改造Seurat包的DoHeatmap函数？](https://www.jieandze1314.com/post/cnposts/change-doheatmap/)】
- [改造inferCNV的热图](https://github.com/reedliu/scRNA-codes/tree/master/2020-1-9-inferCNV-heatmap)【配套说明：[如何改造inferCNV的热图？](https://www.jieandze1314.com/post/cnposts/diy-infercnv-heatmap/)，[来吧，自定义你的热图](https://www.jieandze1314.com/post/cnposts/diy-infercnv-heatmap-2/)】 

### Nice Readings_推荐阅读

#### tutorials_网络教程

- [Getting started with Cell Ranger](https://davetang.org/muse/2018/08/09/getting-started-with-cell-ranger/) by Dave TANG

- [scRNASeqPipeline](https://github.com/tallulandrews/scRNASeqPipeline) by tallulandrews

- [A workflow for single cell RNA-seq data analysis](http://research.fhcrc.org/content/dam/stripe/sun/software/scRNAseq/scRNAseq.html) by Wei Sun

- [singleCellSeq](https://github.com/jdblischak/singleCellSeq) on GitHub
- [ECCB 2018 Single Cell Tutorial](https://github.com/fmicompbio/SIB_scRNA-seq_Tutorial_2018) of SIB course teaching

#### scRNA tools_工具相关

- [software packages of awesome-single-cell by Sean Davis](https://github.com/seandavi/awesome-single-cell) 

#### scRNA experimental design_实验设计



#### scRNA QC_质控

[2016_Classification_of_low_quality_cells_from_single-cell_RNA-seq_data.pdf](https://github.com/reedliu/scRNA-codes/blob/master/scRNA-papers/2016_Classification_of_low_quality_cells_from_single-cell_RNA-seq_data.pdf) 

#### scRNA-seq normalization_标准化



#### scRNA-seq clusering_聚类算法



#### scRNA batch effect_批次效应处理



### Papers_推荐文献

- [Single-cell RNA-sequencing: The future of genome biology is now](https://github.com/reedliu/scRNA-codes/blob/master/scRNA-papers/2017-Single-cell-RNA-sequencing-The-future-of-genome-biology-is-now.pdf), 2017 RNA Biol. [**Recommend**] 综述
-