lieberinstitute / pths_interneurons

genomics analyses of PTHS mouse models investigating interneuron populations

PTHS_interneurons

Genomics analyses of PTHS mouse models investigating interneuron populations. by BaDoi Phan (@ badoi dot phan at pitt dot edu)

Methods

The Tasic_2018_mouse_single-cell folder contains scripts to perform

• Cell type-specific expression analyses
• Cell type deconvolution analyses

scripts

0a. Download script to grab Tasic et al 2018, Nature

0b. Script to tidy Tasic et al data into R and Bioconductor

1. Script to find marker genes for Tasic et al cell types

2. Script for Cell type-specific Expression Analyses

3a. Script to prepare bulk and scRNA data for deconvolution analyses

3a. Script to perform deconvolution of bulk RNA-seq samples with scRNA-seq markers

4. Script to visualize deconvolution cell types from PTHS samples

outputs

The Tasic_2018_mouse_single-cell/plots folder contains source plots for CSEA and deconvolution figures. The Tasic_2018_mouse_single-cell/tables folder contains numerical and tables underlying the figures.