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
Mathematica code for Astrocytes mediate the dopaminergic modulation of tonic GABAergic signaling in substantia nigra
Mathematica notebook containing functions used to measure spikerates, draw histograms, and extract current traces from Clampfit raw data exports.
Code used to analyze striatum population dynamics during isometric forelimb actions
Code used for analysis and figures for paper titled: "Striatal ensembles specify and control granular forelimb actions".
TEsingle Software
Software to analyze TE expression in single cell/single nuclei RNA-seq datasets.
TEsingle pipeline for analysis of Martirosyan dataset
Code to analyze Martirosyan et al. substantia nigra single nuclei RNA-seq dataset with TEsingle.
TEsingle benchmarking pipeline
Code to perform benchmarking of simulated single cell/nuclei RNA-seq datasets with TEsingle and other scRNA-seq software.
Copica, an open-source easy-to-use protein copy number mass spectrometry database
Advances in mass spectrometry allow profiling proteome with 10 ng material. Copica database aids in analyzing and comparing protein abundance in cells and tissues, highlighting specific proteins and enabling easy comparison of datasets.
CURTAIN, A WEB-BASED TOOL FOR DATA VISUALIZATION AND EXPLORATION OF MASS SPECTROMETRY-BASED PROTEOMICS
Curtain is a tool for sharing, visualizing, and analyzing mass spectrometry data, designed for non-experts. It allows easy data sharing via web links and displays differential analysis results in interactive plots.
CURTAIN-PTM, A WEB-BASED TOOL FOR DATA VISUALIZATION AND EXPLORATION OF MASS SPECTROMETRY-BASED PROTEOMICS (POST TRANSLATIONAL MODIFICATIONS)
Curtain is a tool for sharing, visualizing, and analyzing proteomic and PTM MS data. It allows easy sharing of data via web link, displays results in interactive plots, and enables analysis of protein groups and structure. Free and open-source.
Cactus
Cactus (10.5281/zenodo.7351087) manages session data for curtain and curtainptm backends, handling saving and loading operations efficiently.
VariantAnalysis: Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease
Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease
Code – bulkRNA-seq data from WT, ATP13A2 c.1306
Code - bulkRNA-seq data from WT, ATP13A2 c.1306 related to "ATP13A2 Loss of Function-Driven Polyamine Dysregulation Induces SAM Depletion and Epigenetic Astrocyte Toxicity"
bisulfite sequencing
bisulfite sequencing related to "ATP13A2 Loss of Function-Driven Polyamine Dysregulation Induces SAM Depletion and Epigenetic Astrocyte Toxicity"
bulkATAC-seq data from WT, ATP13A2 c.1306
bulkATAC-seq data from WT, ATP13A2 c.1306 related to "ATP13A2 Loss of Function-Driven Polyamine Dysregulation Induces SAM Depletion and Epigenetic Astrocyte Toxicity"
Mitochondrial Proteostasis Cryo-ET Analysis
Collection of scripts used for the analysis of cryo-ET data in Ehses et al., 2026. The code, written in MATLAB 2019b, includes pipelines for tomogram pre-processing and reconstruction as well as particle quantification.
R Code used in “Sex-Specific Microglial Responses to Glucocerebrosidase Inhibition: Relevance to GBA1-Linked Parkinson’s Disease”
R Code used in "sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease."
