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