Templates with revision indicates that the components or processes have undergone comprehensive parameterization and testing.

Templates with revision indicates that the components or processes are currently being tested. There is some test data available, but there are parameters that need to be set up manually within the code.

Templates with revision indicates that the components or processes are not fully tested. There is no test data available, parameters need to be set up manually within the code, and specific code changes are required based on the data used.

Read main page to know how to collaborate with us.

Guideline for scRNAseq analysis

Make sure there is a valid project name, and modify information.R with the right information for your project. You can use this file with any other Rmd to include the project/analysis information.

• Set the working directory to this file level. We recommend to use Projects in Rstudio.
• Use install_dependencies.R to install all packages used in these reports.

nf-core

cellranger outputs are in your output directory under results/cellranger.

running cell-ranger by yourself

pre-process-w-cellranger.md contains step by step guidelines on how to run cellranger.

Then, the scripts/seurat_init.R script contains all the pieces to go from cellranger output to Seurat obj. It is assuming a mouse genome. Alternatively, if you have an especially large single cell dataset, you may wish to construct a Seurat object where the counts matrix remains stored on-disk and is not loaded into R memory. The scripts/seurat_ondisk.R script can assist with this.

Quality Assessment

scATAC

The Rmd that helps to visualize ATAC metrics is 01_quality_assessment/scATAC_QC.Rmd.

scRNA

Currently we are working on deploying a shiny app to inspect the single cell object and find the best cut-offs for filtering. The Rmd that helps to visualize the before and after is 01_quality_assessment/scRNA_QC.Rmd.

Integration

02_integration/norm_integration.rmd is a template with guidelines on how to work with multiple samples. It compares log2norm vs SCT, work with SCT by samples to remove batch biases better, provide options for integration between CCA and Harmony. As last step, it contains cell type clustering and visualization to help decide the best parameters.

Differential Expression

Read full documentation at 02_differential_expression/README.md.

• pseudobulk approach: 02_differential_expression/scRNA_pseudobulk.Rmd is a template that performs pseudobulk differential expression analysis using DESeq2.

• MAST - single cell approach: 02_differential_expression/scRNA_MAST.Rmd is a template to visualize differentially expressed genes (DEG) results generated from MAST analysis. ## Compositional Analysis

Compositional Analysis

04_compositional/propeller.Rmd and 04_compositional/sscomp.Rmd are templates to run compositional analysis with two different methods. comp.png is an example of sccomp.Rmd analysis.