RNAScope_prop: Cell Type Proportions estimated from RNAScope

In LieberInstitute/DeconvoBuddies: Helper Functions for LIBD Deconvolution

Cell Type Proportions estimated from RNAScope

Description

Cell type proportion estimates from high quality images from Huuki-Myers et al., bioRxiv, 2024, doi: https://doi.org/10.1101/2024.02.09.579665.

Usage

RNAScope_prop

Format

A data.frame object.

Details

11.49 kB

These are the columns of the data.frame object:

• SAMPLE_ID : DLPFC Tissue block + RNAScope combination.

• Sample : DLFPC Tissue block (Donor BrNum + DLPFC position).

• Combo : RNAScope probe combination, either "Circle" marking cell types Astro Endo, Inhib, or "Star" marking Excit, Micro, and OligoOPC.

• cell_type : The cell type measured.

• Confidence : Image confidence, this dataset has been filtered to the high & Ok confidence images.

• n_cell : the number of cells counted for the Sample and cell type.

• prop : the calculated cell type proportion from n_cell.

• n_cell_sn : number of nuclei in the corresponding snRNA-seq data.

• prop_sn : cell type proportion from the snRNA-seq data.

Source

https://github.com/LieberInstitute/brainstorm/blob/master/data-raw/RNAScope.R

LieberInstitute/DeconvoBuddies documentation built on Nov. 1, 2024, 11:58 a.m.