Single Cell
These code block examples can be used to generate a Single-Cell figure by using a .fpkm file as seen in VisCom.
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.
Warning
If you are using a path on the HPC, the file must exist in a directory in the
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:
- 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/.