Single Cell RNA Seq Training Seminar
In partnership with 10X Genomics
Monday and Tuesday, 1st and 3rd of March
Instructors: Dr David Powell, Dr Paul Harrison, Dr Nick Wong, Dr Dee Deveson-Lucas, Nitika Kandhari, Peinan Zhao, Patrick Deng
Day Two: Using Seurat (SingleR and Monocle)
This workshop, conducted by the Monash Bioinformatics Platform, will cover how to extend analysis to contemporary third-party tools, Seurat and Monocle. We will be walking through the 3K PBMC Dataset Tutorial and extend this to Monocle with some trajectory analysis.
Important links:
Recommended Computer Requirements:
System Requirements:
Windows:
- Windows 8.1 (64-bit) or later
- 4GB RAM
- SSD storage highly recommended
- Updated video/display drivers recommended
macOS:
- macOS 10.15 (Catalina) or later
- 4GB RAM
- SSD storage highly recommended
Install latest versions of:
- R
- RStudio
- Seurat
- SeuratWrappers
- Monocle
Venue: Virtual workshop conducted via Zoom with breakout rooms. Zoom links will be provided after registration is complete.
Suggested Further Reading Material
- Orchestrating Single Cell Analysis with Bioconductor - this book teaches single cell analysis with the bioconductor ecosystem of packages rather than Seurat. Regardless of your preference for Bioconductor or Seurat, it provides an excellent grounding and further depth and rationale behind each step of a single cell analysis.
- Seurat tutorials for gene expression, spatial & multimodal analysis
- Getting started with Signac - the sibling package to Seurat for scATAC analysis
- Monocle documentationn for trajectories
- Cell Annotation with SingleR
- VDJ analysis with Immcantation
Useful links arising from the discussion during the workshop
- 10x Genomics link to ribosomal protein expression
- 10x Genomics link to mitochondrial gene expression
- scRNA Tools, catelogue of tools for scRNA Seq analysis
Data interpretation
- Interactive website explaining UMAP and comparision to t-SNE.
- OSCA, dimensionality reduction interpretation
Data tools and visualisation
- scTransform Vignette
- Link to the workflowr library
- iSEE Bioconductor library, interactive explorer
- ShinyCell makes interactive Shiny app from Seurat output
- iCellR interactive data explorer
- Diffusion maps for single cell instead of umaps
Papers
- Doublet cell detection method benchmarking paper.
- From Louvain to Leiden: guaranteeing well-connected communities