SCNPrep is an R package to convert Seurat object into Single-cell Navigator compatible json files.

For full documentation of json files, please, refer to https://artyomovlab.wustl.edu/scn/docs/docs/.

To install the package use

devtools::install_github("ctlab/SCNPrep")

Single-cell Navigator requires several files to be present for each dataset:

General (these files are required):

• dataset.json (required) contains description of the dataset.
• plot_data.json (required) contains calculated information about every cell (like clustering and tSNE coordinates) as well as precalculated annotations (like cluster borders)

Expression data:

• exp_data.json contains gene names and cell barcodes in the same order as they appear in expression matrix, as well as number of total UMIs in the cell.
• data.h5 is an expression (count) matrix. HDF5 allows storing counts effectively: since for the scNavigator we mostly need to look expression of a gene in the datasets, HDF5 can effectively compress columns of integers.

Markers:

• markers.json json file describing gene expression markers (optional)

Gene signature search:

• species.modules.gmt where species are hs, mm or rn depending on your dataset
• modules.annotation.json describing each of the modules present in the species.modules.gmt

Extra files:

• files is a directory (next to dataset.json) where you can put any additional files of choice (optional)

You can use this package to generate all these files for Seurat object.

library(SCNPrep)

## below we assume that `object` is Seurat object after running Seurat v3 pipelines.

migrateSeuratObject(object, 
                    species="mm", 
                    outdir = "./out", 
                    public = T, 
                    generateMarkers = T,
                    token="SRS5753114")