单细胞学习资源

哈佛大学单细胞课程

• Part 1
  • Introduction to scRNA-seq
  • Raw data to count matrix
• Part II
  • Quality control set-up
  • Quality control
  • Overview of Clustering Workflow
  • Theory of PCA
  • Normalization and regressing out unwanted variation
• Part III
  • Integration
  • Clustering
  • Clustering quality control
  • Marker identification
  • Solution to exercises in above lessons

拟时间分析

• Temporal Reconstruction Algorithm
  • Manuscript:Reconstructing the temporal ordering of biological samples using microarray data
• Monocle / Monocle 2 / Monocle 3 / Census
  • Software:https://bioconductor.org/packages/release/bioc/html/monocle.html
  • Monocle manuscript:The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
  • Census manuscript:Single-cell mRNA quantification and differential analysis with Census
  • Monocle 2 manuscript:Reversed graph embedding resolves complex single-cell trajectories
  • Monocle 3 manuscript:The single-cell transcriptional landscape of mammalian organogenesis

10X

https://www.10xgenomics.com/support

单细胞数据

• SRP201551
• GSE132802
• scDesign2
• scDesign3

• 单细胞文章复现
• 单细胞转录组分析常用软件集合
• 单细胞转录组分析常用软件集合Github
• 2021单细胞文献
• 2020单细胞文献
• 2019单细胞文献

https://bookdown.org/ytliu13207/SingleCellMultiOmicsDataAnalysis/
01.上游分析流程
02.课题多少个样品，测序数据量如何
03. 过滤不合格细胞和基因（数据质控很重要）
04. 过滤线粒体核糖体基因
05. 去除细胞效应和基因效应
06.单细胞转录组数据的降维聚类分群
07.单细胞转录组数据处理之细胞亚群注释
08.把拿到的亚群进行更细致的分群
09.单细胞转录组数据处理之细胞亚群比例比较

https://mp.weixin.qq.com/s/Kn3f48bIkYDoEuSIjs1sFQ

https://mp.weixin.qq.com/s/dEcADJ6S3F-yHUGBGlW33g

pbmc.rds