A R Shiny App to ease single-cell analysis

Aim

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The aim of this project is to build a minimalist, but flexible R Shiny application to aid wet lab scientist to analyse their single cell data.

The analysis to be included are;

1. Single cell RNAseq clustering workflow
2. Single cell RNA-seq data integration
3. Single cell ATAC-seq analysis
4. Integration of scRNA-seq and scATAC-seq data
5. Multimodal analysis using cite-seq
6. Automatic cell labelling

Supported data formats

1. 10X Cell Ranger (.HDF5)
2. loom
3. rds
4. AnnData (.h5ad)
5. .mtx, name your files as; features_.tsv, matrix_.mtrx and genes_*.tsv

Status

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• scRNA-seq clustering workflow
• Automatic cell labelling
• scATAC-seq workflow
• Doublet removal
• scRNA-seq data integration
• scRNA-seq + scATAC seq data integration
• Multimodal analysis using cite-seq

Packages

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1. Seurat
2. Signac (scATAC-seq)
3. DoubletFinder (Removal of doublets)
4. SingleR (Automatic labelling of cells)
5. celldex (Autmatic labelling of cells)

Usage

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Currently the program can only be used by cloning the repository and running locally

The next step would be to provide it as a docker image to ease its distribution.