Getting Started

For advanced users (computational Biologists) using R, please read the following FAQ for import data objects

How can I load my analysis or Seurat Object (for R user) into single cell explorer database?

You can export results from seurat object to csv files including the expression matrix and embedded data (UMAP or t-SNE) and metadata (study information) firstly using import Seurat object guide , put three files in one folder, followed by a python script to load three files into MongoDB. load to MongoDB

How can I load Loom files (for R user) into single cell explorer database?

You can export results from loom files to csv files including the expression matrix and embedded data (UMAP or t-SNE) and metadata (study information) firstly using import Loom file , put three files in one folder, followed by a python script to load three files into MongoDB. The latest version of lommpy (Version 2.0.17) has backward-compatible issues for a few published single cell data, therefore we do not provide example scripts using loompy at this stage. load to MongoDB

Can I use my own database?

Yes, as long as you followed our walkthrough examples, You can host MongoDB in any server as long as it is accessable for the single cell explorer application. You can dump your old data into MongoDB using our import examples described above. Basically you just need to create three csv files for each map, then load it. load to MongoDB