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
Long-read RNA seq analysis using Talon
This is a pipeline that takes fastq data as input, generates fastq stats using nanostat, performs fastq processing and filtering using pychopper, maps the reads to the genome using minimap2, and uses talon to assemble and quantify transcripts.
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
ggtranscript simplifies visualizing transcript structure with new geoms like range(), intron(), junction(), and junction_label_repel(). It extends ggplot2's flexibility to create informative plots for publication.
TX2P – Transcript to protein
TX2P automates mass spectrometry data integration in long-read RNA-sequencing by predicting open reading frames, translating them into peptides, and searching for proteins in mass spec datasets with MetaMorpheus.
napari-polcam
A plugin for napari is available to handle and display polarization camera data efficiently.
Direct visualisation of Alpha-Synuclein Oligomers in Human Brain
Direct visualisation of Alpha-Synuclein Oligomers in Human Brain
pyRASP
The package "pyRASP" is a set of Python classes that can be run from scripts, interactive notebooks, and so on to analyze microscopy data. An example notebook is provided, showing user analyses.
RNAseqProcessing
Comparison of RNA QC tools trimmomatic and fastp. Additionally, scripts provided for RNA-seq processing steps, covering QC, alignment, and quantification.
R Code (RNA editing)
The repository at https://github.com/karishdsa/ipscAstrNeurCocul contains single-cell and bulk RNA sequencing analysis of the cell culture models
Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
This repository contains analysis code for the publication found here, which explored the response of astrocytes, neurons and astro-neuronal co-cultures to alpha-synuclein oligomers.
LR project, R code
The LR project explores ligands and receptors in cross-disease risk. Access public datasets listed in resources/KRT.txt. Use provided libraries and scripts in order (00 to 08) to reproduce results and plots.
SNCA transcript diversity in neurons
This repository contains the code used to generate the plots used in the SNCA transcript expression and ASO modulation manuscript.
LR Project
The LR project aims to study ligands and receptors in cross-disease risk. To reproduce findings, access public datasets and databases listed in KRT.txt. Use provided libraries and run scripts sequentially from 00 to 08 for plots and results.
LR Project, Python code
The LR project investigates ligands and receptors in cross-disease risk. Access public datasets listed in resources/KRT.txt. Use libraries and scripts in order (00 to 08) to reproduce findings. Custom library "mellon" available in the repository.
Astrocyte Editing
Analysis code for studying astrocytes, neurons, and astro-neuronal co-cultures' response to alpha-synuclein oligomers is split between two repositories: on RNA sequencing, the other examines RNA editing in cell models and post-mortem brain samples.
cameraCalibrationCMOS
Camera calibration in MATLAB helps convert pixel values to photoelectrons or photons for accurate image comparisons. Regular calibration is recommended due to gain drift in EMCCD cameras.
