Welcome to the Cancer Data Science Shared Resource (CDS-SR) 2022 scRNA-seq workshop GitHub page! This page contains lecture slides, coding scripts, and other documents over topics discussed in this workshop.
Dates: April 18-19, 2022
The example datasets and recordings used in this workshop are found in the Google Drive link here:
https://drive.google.com/drive/folders/1T2YJcnFyNdmY8ohfN4hAu4JVgQFyZ-v2?usp=sharing
Folders:
data = contains tables used in Section 2
objects = contains Seurat objects used in Section 2
plots = contains plots that were made for both Section 1 and 2
Lecture slides for Section 1 and coding scripts for both sections can be found here:
https://github.com/tstephie/UMICH-CDS-SR-scRNA-seq-Workshop-2022/tree/main/section_1
Section 2's R coding scripts (.rmd and .html) can be found here:
https://github.com/tstephie/UMICH-CDS-SR-scRNA-seq-Workshop-2022/tree/main/section_2/code
Please take a look at the document here of how to setup R, Rstudio, and packages:
https://github.com/tstephie/UMICH-CDS-SR-scRNA-seq-Workshop-2022/blob/main/section_2/How%20to%20Setup%20for%20Section%202.docx
| Activity | Powerpoint File |
|---|---|
| Introduction to scRNA-seq Technology | CDS-SR scRNA-seq workshop_Introduction to scRNA-seq.pptx |
| CellRanger Pipeline | CDS-SR scRNA-seq workshop_scRNA-seq Analysis_intro_align_quant.pptx |
| Seurat - Standard Pipeline | CDS-SR scRNA-seq workshop_scRNA-seq Analysis_seurat_intro_standard_pipeline.pptx |
| Seurat - Integration Pipeline | CDS-SR scRNA-seq workshop_scRNA-seq Analysis_seurat_integration_pipeline.pptx |
| Seurat - Cell Annotation | CDS-SR scRNA-seq workshop_scRNA-seq Analysis_seurat_cell_annotations.pptx |
| Additional Downstream Analyses | CDS-SR scRNA-seq workshop_scRNA-seq Analysis_seurat_additional_downstream_analyses.pptx |
| Activity | HTML/RMD File |
|---|---|
| Introduction to R & Importing and Creating Seurat Objects | cds_scrnaseq_workshop_2022_section2_analysis_import.html/rmd |
| Standard Pipeline | cds_scrnaseq_workshop_2022_section2_analysis_standard_pipeline.html/.rmd |
| Integration Pipeline | cds_scrnaseq_workshop_2022_section2_analysis_integration_pipeline.html/.rmd |
| Cell Annotation | cds_scrnaseq_workshop_2022_section2_analysis_cell_annotation.html/.rmd |
| Cell Subpopulation Analysis & Pathway Analysis | cds_scrnaseq_workshop_2022_section2_analysis_subtype_pathway.html/.rmd |