README.md

In ctlab/SCNPrep: Preparing Seurat object for use in scNavigator

SCNPrep

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/.

Installation

To install the package use

devtools::install_github("ctlab/SCNPrep")

Usage

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")

ctlab/SCNPrep documentation built on Dec. 19, 2021, 7:02 p.m.