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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Output Type
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Program
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CRN Team Name
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Theme
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
circRNA Custom Code
Custom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.
powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Easy-to-use web application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
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.
Single-cell-RNA-seq-of-the-CRISPR-engineered-endogenous-tauopathy-model
scRNA-seq data analysis workflow Step1: bash cellranger_mkfastq.sh This will generate fastq files. Step2: bash cellranger_count_submission.sh This will call another bash file “cellranger_count.sh” and generate count tables Step3: bash…
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.
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.
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.
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.
