Software for data analysis used in the manuscript “Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinson’s disease” (doi: 10.1073/pnas.2402206121)
Output Details
Description
Data Preprocessing: Seurat [version 3, https://satijalab.org/seurat/] was used for single-cell analysis (https://doi.org/10.5281/zenodo.10470951). Quality control steps were performed to identify and remove cells that were potential outliers. This included removing potential multiplets using “DoubletFinder” [https://github.com/chris-mcginnis-ucsf/DoubletFinder] and “cells” that displayed high mitochondrial gene expression (using the subset function to remove clusters with high expression of “MT-” genes). The data were then normalized and log-transformed (using the “LogNormalize” method), and counts were scaled. All files, including the scripts used for Seurat gene expression analyses are available on Dryad (https://doi.org/10.5061/dryad.pk0p2ngvp).
Identifier (DOI)
10.5281/zenodo.10470950
