单细胞至少得培训3天及以上

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单细胞成为了科研热点，是毋庸置疑的，所以很多商业培训机构跟风开始举办各式各样的培训班，粗略看了下课表，简直~~~

更有趣的是，根据我们粉丝中的一些参加过培训班的学员，大多数培训班基本上都是蜻蜓点水的介绍一些PPT常识。

有必要介绍给大家一个真正的单细胞培训，基本上涵盖了我的的全网第一个单细胞课程（基础）满一千份销量就停止发售 内容，就是一些R包的认知，包括 scater,monocle,Seurat,scran,M3Drop 需要熟练掌握它们的对象，：一些单细胞转录组R包的对象 ，分析流程也大同小异：

  • step1: 创建对象
  • step2: 质量控制
  • step3: 表达量的标准化和归一化
  • step4: 去除干扰因素(多个样本整合)
  • step5: 判断重要的基因
  • step6: 多种降维算法
  • step7: 可视化降维结果
  • step8: 多种聚类算法
  • step9: 聚类后找每个细胞亚群的标志基因
  • step10: 继续分类

就是Single cell RNA-seq data analysis with R，课程由欧盟的面向生物信息的欧洲生命科学基础设施（ELIXIR）的 ELIXIR-EXCELERATE项目 全额资助，所以是免费的。羡慕在欧洲的朋友们！

Monday 27.5.2019

  • Introduction and experimental design (Åsa Björklund, Jules Gilet)
  • QC, data preprocessing (Åsa Björklund)
  • Normalisation and batch effect correction (Heli Pessa, Bishwa Ghimire)
  • Data integration (CCA, MNN, dataset alignment) (Ahmed Mahfouz)

Tuesday 28.5.2019

  • Dimensionality reduction (PCA, tSNE and UMAP) (Paulo Czarnewski)
  • Clustering (Ahmed Mahfouz)
  • Differential gene expression analysis (Ståle Nygård)

Wednesday 29.5.2019

  • Cell type identification (Philip Lijnzaad)
  • Trajectories/Pseudo-time (Paulo Czarnewski)
  • Spatial transcriptomics (Jeongbin Park and Lars Borm)

具体课表是：

Monday 27.5.2019
 09:00-09:45 Lecture: Introduction and experimental design (Jules Gilet)
 09:45-10:15 coffee break
 10:15-11:00 Lecture: Quality control (Åsa Björklund)
 11:00-12:00 Labs: Quality control (Åsa & Jules). Bonus exercise (not to be done in the class): Sequencing QC and Ikura pipeline (Jules).
 12:00-13:00 lunch
 13:00-13:45 Lecture: Normalisation and removal of confounding factors 
 13:45-14:30 Labs: Normalisation and removal of confounding factors (Heli & Bishwa)
 14:30-15:00 coffee break
 15:00-15:45 Lecture: Data integration (Ahmed Mahfouz)
 15:45-17:00 Labs: Data integration (Ahmed Mahfouz)
Tuesday 28.5.2019
 09:00-09:45 Dimensionality_reduction (Paulo Czarnewski)
 09:45-10:15 coffee break
 10:15-11:00 Labs: Continue from Data integration, (Rmd file)
 11:00-12:00 Lecture: Clustering (Ahmed Mahfouz)
 12:00-13:00 lunch
 13:00-14:30 Labs: Clustering, (Rmd file) (Ahmed Mahfouz)
 14:30-15:00 coffee break
 15:00-17:00 Differential expression, (Rmd file 1), (Rmd file 2) (Ståle Nygård)
Wednesday 29.5.2019
 09:00-11:00 Lecture: Cell type identification (Philip Lijnzaad)
 09:45-10:15 coffee break
 10:15-11:00 Labs: Cell type identification, (Rmd file) (Philip)
 11:00-12:00 Lecture: Trajectories/Pseudo-time I (Paulo, Jules). Labs
 12:00-13:00 lunch
 13:00-14:00 Trajectories/Pseudo-time II (Paulo, Jules). Labs
 14:00-14:30 Lecture: Spatial transcriptomics I (Lars Borm)
 14:30-15:00 coffee break
 15:00-16:30 Lecture: Spatial transcriptomics II (Lars Borm & Jeongbin Park)
 16:30-17:00 Discussion and questions
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