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.
ASAP CRN Cloud Release Notes – Version 2.0.0
Version: 2.0.0 Release Date: December 11, 2024 This release notes document provides a concise overview of the updates and enhancements introduced in Version 2.0.0 of the CRN Cloud platform.
ASAP CRN Cloud Release Notes – Version 1.0.0
Version: 1.0.0 Release Date: June 25, 2024 This release notes document provides a concise overview of the updates and enhancements introduced in Version 1.0.0 of the CRN Cloud platform.
ASAP CRN Cloud Release Notes – Version 1.0.0-beta
Version: 1.0.0-beta Release Date: March 6, 2024 This release notes document provides a concise overview of the updates and enhancements introduced in Version 1.0.0-beta of the CRN Cloud platform.
ASAP CRN Cloud Release Notes – Version 0.0.1
Version: 0.0.1 Release Date: November 10, 2023 This release notes document provides a concise overview of Version 0.0.1 of the CRN Cloud platform.
Gene expression profile at single cell levels of the cells from the controls and tau P251L Drosophila brain
Tau protein's role in Alzheimer's disease was studied by introducing a human tau mutation into Drosophila using CRISPR. Single-cell RNA sequencing helped identify genes and pathways involved in tauopathy.
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.
ASAP Parkinson Cell Atlas in 5D (PD5D)
The PD5D Atlas deciphers Parkinson's disease molecular blueprint using brain space, disease stage, and cell types dimensions. It includes various omics data and clinical scales to analyze PD progression from healthy aging to Lewy body neuropathology.
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.
Developing Allelic Imbalance Analysis from Single-Nucleus RNA-Seq Data
Allele-specific expression (ASE) analysis in single-nucleus RNA-seq (snRNA-Seq) helps study genetic variation impact on RNA expression. Experimental and computational choices can enhance ASE analysis results.
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.
