Single Cell

Last updated: 3 years ago (view history), Time to read: 1 mins

Description

These code block examples can be used to generate a Single-Cell figure by using a .fpkm file as seen in VisCom.

Use: A data driven dimensional reduction method used to display single cell RNA seq data from a large number of cells. ProteinPaint Google Docs

URL Key Example

This currently is not supported with a url key at this time.

tip

If you are using a path on the HPC, the file must exist in a directory in the /tp directory. For more details, see our manage data section.

File Key Example

Be sure to update lines 6 and 7 

{
 "singlecell": {
 	"genome": "hg19",
 	"jsonfile": "proteinpaint_demo/hg19/singlecell/singlecell.json"
	}
}

If you need an example of how the JSON should be formatted, you can:

  1. Example 1: Go to https://proteinpaint.stjude.org/

    • Select Single Cell

      • It will load an Example

      • Select Code

        • Review the JSON formatting

Furthermore, you can have your excel sheet converted to JSON; there are many ways to do this, but one example is using BeautifyTools and debug by using https://jsonlint.com/.