reedliu / scRNA-codes

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：2017-Identifying_cell_populations_with_scRNASeq.pdf

Scripts_常用脚本

• cellranger count操作
• 校正批次效应
• seurat V3操作（以PBMC 2700为例）
• seurat组合10X数据
• monocle2使用
• monocle3使用
• 用几个R包寻找HVGs
• Bioconductor-scRNA之基础操作
• mouce_c1下游分析全套
• 改造Seurat的DoHeatmap函数 【配套说明：如何改造Seurat包的DoHeatmap函数？】
• 改造inferCNV的热图【配套说明：如何改造inferCNV的热图？，来吧，自定义你的热图】

Nice Readings_推荐阅读

tutorials_网络教程

• Getting started with Cell Ranger by Dave TANG

• scRNASeqPipeline by tallulandrews

• A workflow for single cell RNA-seq data analysis by Wei Sun

• singleCellSeq on GitHub

• ECCB 2018 Single Cell Tutorial of SIB course teaching

scRNA tools_工具相关

• software packages of awesome-single-cell by Sean Davis

scRNA experimental design_实验设计

scRNA QC_质控

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, 2017 RNA Biol. [Recommend] 综述