OSU-BMBL/bmbl-class-notebooks

BMBL-notebooks

Table of contents

1. Introduction to OSC
2. Introduction to R programming language & R markdown
3. RNA-seq data analysis (DESeq2)
4. Single-cell RNA-seq single sample analysis (Seurat)
5. Single-cell RNA-seq multi sample analysis (Seurat)
6. ChIP-seq data analysis (ChIPseeker)
7. Single-cell ATAC-seq general analysis (Seurat & Signac)
8. Single-cell ATAC-seq general analysis (ArchR)
9. Single-cell ATAC-seq cis-regulatory networks & co-accessibility analysis (cicero)
10. Single-cell ATAC-seq cis-regulatory topics * cell states analysis (cisTopic)
11. Single-cell multi-omic data analysis (Seurat)
12. Spatial transcriptomics data analysis (Giotto)
13. Spatial transcriptomics clustering analysis (BayesSpace)
14. Spatial transcriptomics deconvolution analysis (Spotlight)
15. Single-cell immune profiling data analysis (scRepertoire)
16. Single-cell RNA-seq cell-cell communication analysis (CellChat)
17. Single-cell RNA-seq data integration (Seurat)
18. Single-cell RNA-seq cell type label transfer using atlas data (scANVI)
19. TCGA survival analysis

About

Maintainer: Cankun Wang

Authors:

• Cankun Wang
• Jiaxin Yang
• Yingyi Zhu
• Shicong Wang
• Yuzhou Chang

Repository material are inspired by the following courses or workshops:

• Bioinformatics Training at the Harvard Chan Bioinformatics Core
• UC Davis Bioinformatics core workshop
• SciLifeLab Analysis of RNA-Seq Data
• Seurat vignettes
• Signac vignettes

Contact us: qin.ma@osumc.edu