Output Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
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ASAP CRN Cloud Release Notes – Version 4.0.0
ASAP CRN Cloud released version 4.0.0 with expanded datasets including Human Postmortem-derived Brain Sequencing and Mouse datasets. New harmonized collections and individual datasets were added, enhancing research possibilities.
Bolen CosMx human Colon RNA and Protein code
Repository for the paper "Spatial single-cell multiomics..." includes CosMx assays, README files with scripts/data for analysis, and computational environment requirements. It also features a tissue microarray image showing morphology markers.
Code R script related to doi.org/10.1038/s41531-025-01063-3
Severe GBA1 variants are linked to Parkinson's disease, impacting counseling and clinical trials. Access R script at doi.org/10.1038/s41531-025-01063-3 for more details.
Generation of knock-in Cre and FlpO mouse lines for basal ganglia and dopamine neuron investigation (CODE)
The software contained in this repository was used to analyze the whole-cell electrophysiology recordings of striatal spiny projection neurons and midbrain dopamine neurons.
scAlleleExpression: R package for downstream analysis of allele specific expression single cell data
An R package for investigating Cell Type specific regulatory genetics using single cell or nuclei allele specific expression data. It loads ASE pipeline output, performs ASE analysis, and works with various ASE pipelines.
scASE_py: Python pacakge for loading single cell allele specific data
Python package for single cell allele-specific expression (ASE) output manipulation available at https://github.com/seanken/ASE_pipeline. R package for downstream analysis at https://github.com/seanken/scAlleleExpression.
CellLevel_QC: Extracting cell level QC metrics from CellRanger barcoded bams
Java code in this repository retrieves cell level mapping data (intronic reads, intergenic reads, multimapped reads, etc) from CellRanger output. Compatible with CellRanger v5 and v6, may work with newer versions and Spaceranger output.
Single cell allele specific expression processing pipeline for long read data
Pipeline processes long read single cell/nucleus 10X data (ONT, PacBio, MAS-Seq) to generate gene/isoform-level allele-specific expression (ASE) counts.
Analyses of metabolite profiling of Drosophila Parkinson’s Disease model for identifying novel glial-based therapeutic targets
Genetic screening and metabolomics show glial adenosine metabolism as a potential treatment for Parkinson’s disease. Analysis includes measuring metabolite levels in synuclein expressing/control fly brains with different methods.
HYX990205/ReRx: Drug Repurposing for Parkinson’s Disease
Toolkit for drug repurposing analysis used in the preprint: "Drug Repurposing for Parkinson's Disease: A Large-Scale Multi-Cohort Study" Find more at https://doi.org/10.1101/2025.05.20.25327943.
TheDongLab/EVscope: v1.0.0
EVscope is a tool for analyzing extracellular vesicle RNA sequencing data, addressing challenges like low yield and contamination. It includes quality control, alignment, circular RNA detection, expression quantification, and reporting.
SIFT based MATLAB script [Hanna et al 2024]
SIFT based MATLAB script used in the preprint Hanna et al 2024
Python code: Figure generating script [Hanna et al 2024]
Python code: Figure generating script used in the preprint Hanna et al 2024
ImageJ code: Analysis script_0 [Hanna et al 2024]
ImageJ code: Analysis script_0 used in the preprint Hanna et al 2024
Script for image quantification [Wang et al 2025]
Script for image quantification used in Wang et al 2025
