Single Cell RNA Seq Training Seminar
Instructors: Adele Barugahare & Dr Paul Harrison & Dr Laura Perlaza-Jimenez
Using Seurat (SingleR and Harmony)
This workshop, conducted by the Monash Bioinformatics Platform, will cover how to extend analysis to contemporary third-party tools, Seurat, Harmony and SingleR. We will be walking through the Seurat 3K PBMC Dataset Tutorial and extend this to and SingleR & Harmony for cell annotation and dataset integration.
Important links:
- Installation and Setup instructions
- PBMC Workshop material
- Dimensionality reduction example
- Challenge solutions (no peeking!)
- M1 MacOS installation instructions - only use these if you have an M1 Mac
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
- SingleR
- Celldex
- Harmony
Acknowledgements
This material is mostly based on the Seurat introductory tutorial.
It also draws from material for a workshop provided by QCIF developed by Sarah Williams and Ahmed Mehdi for the Australian Biocommons.
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 previous workshop
- 10x Genomics link to ribosomal protein expression
- 10x Genomics link to mitochondrial gene expression
- scRNA Tools, catalogue 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