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
LiD genetic determinants study under CPH regression models
Code to perform the study of LiD genetic determinants under CPH regression models and functional annotation analyses.
huw-morris-lab/PDD_GWSS
The manuscript by Real et al. investigates the relationship between LRP1B and APOE loci and the onset of Parkinson’s disease dementia, utilizing specific code for analysis.
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.
Proband-NFL Analysis
Code used for the manuscript "Combining biomarkers for prognostic modelling of Parkinson’s disease" by Niro Viijaratnam and colleagues.
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.
Code for splicing-accuracy-manuscript
Code used for manuscript: Splicing accuracy varies across human introns, tissues and age
katiekellyucl/W-PPI-NA-NSL-complex: v1.0.0. W-PPI-NA/NSL_complex
Software for in Silico analysis linking the NSL complex to Parkinson’s disease and the mitochondria (protein-protein interaction data to functional enrichment analysis)
Code for making forest plots for top GWAS loci
This repository contains the script used to create forest plots for top loci [part of code for the PD progression survival GWAS to mortality, Hoehn and Yahr stage 3 or greater (H&Y3+), and dementia].
RHReynolds/neurodegen-psych-local-corr: Code to determine local and global genetic correlations between several neurodegenerative and neuropsychiatric disorders with LAVA and LDSC, respectively.
Code for paper "Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases" that explores local genetic correlations among neurodegenerative and neuropsychiatric diseases.
ensemblQueryR
A package allowing easy integration of Ensembl querying with a user’s R workflow.
LBD-case-case-GWAS
Code used in article: Investigation of the genetic aetiology of Lewy body diseases with and without dementia.
RNAseqProcessing
Comparison of RNA QC tools trimmomatic and fastp. Additionally, scripts provided for RNA-seq processing steps, covering QC, alignment, and quantification.
egustavsson / GBA_GBAP1_manuscript
Code used to generate the plots used in manuscript, "The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1" (DOI: 10.1126/sciadv.adk1296).
manuelatan/PD-survival-GWAS: Release 2.0
Code used for PD progression survival GWAS to mortality, and Hoehn and Yahr stage 3 or greater (H&Y3+).
