This website uses cookies so that we can provide you with the best user experience possible. Cookie information is stored in your browser and performs functions such as recognising you when you return to our website and helping our team to understand which sections of the website you find most interesting and useful.
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.
Code
Long-read RNA seq analysis using Talon
This is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) 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. It is forked from ANNSeq. The link includes the dag of the pipeline.
Themes
Code
TX2P – Transcript to protein
TX2P allows for automated integration of mass spectometry data in long-read RNA-sequencing workflow. It does so by predicting open reading frames for each transcripts within an input GTF/GFF file, translates it into peptide sequences and then searches for those predicted proteins in mass spec datasets using MetaMorpheus.
Teams
Themes
Code
pyRASP
The package “pyRASP” (written in support of https://www.biorxiv.org/content/10.1101/2023.12.18.572148v2) 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.
Teams
Themes
Code
Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
This current repository contains single-cell and bulk RNA-sequencing analysis of the cell culture models utilized in the study.
The repository at https://github.com/aaronwagen/Astrocytes_editing contains the analysis of RNA editing in the cell culture models, as well as in a published dataset of post-mortem brain samples.
Teams
Themes
Code
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 utilized in the study. This current repository contains the analysis of RNA editing in the cell culture models, as well as in a published dataset of post-mortem brain samples.
Teams
Themes
Code
sCMOS calibration software
This is software for calibrating sCMOS cameras, written in MATLAB. The readme file gives instructions on how to record experimental data and use the code to estimate the pixel-dependent offset, gain, variance, and read noise of a sCMOS camera.
Teams
Themes