R code for paper Phenotype of GBA1 variants in individuals with and without Parkinson disease: the RAPSODI study
By onThis is the R code used to produce the results described in the paper "Phenotype of GBA1 variants in individuals with and without Parkinson’s disease: The RAPSODI study"
Code for analysis of ER-phagy in iNeurons via proteomics
By onCode for analysis of ER-phagy in iNeurons via proteomics. Associated with preprint: https://doi.org/10.1101/2023.06.26.546565
Proband-NFL Analysis
By onCode used for the manuscript "Combining biomarkers for prognostic modelling of Parkinson’s disease" by Niro Viijaratnam and colleagues.
Code for splicing-accuracy-manuscript
By onCode used for manuscript: Splicing accuracy varies across human introns, tissues and age
AAV.CAP-Mac analysis code
By onFirst release of AAV.CAP-Mac analysis code and files to generate figures.
ImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections
By onImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections.
Scripts for analysis of total proteomes in response to nutrient stress
By onScripts for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons–DropSeqPipeline8
By onThis is a data processing pipeline for analyzing microwell- or DropSeq-like scRNA-seq data. It can also be used for analyzing pooled plate-based scRNA-seq
Python script used to generate the heatmap representation of identified LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308
By onPython script used to generate the heatmap representation of identified high-confident LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308.
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
By onR package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Neurite_FISH_Quant–Python code for quantification of FISH puncta in neurites
By onThis repository contains Jupyter Notebooks with Python 3 code for quantification of FISH puncta within neuronal dendrites or axons. However, prior identification of FISH puncta in the images (and optional neurite segmentation) is required. We use ImageJ plugins for this purpose, as specified below. The workflow assumes Z-stack, multi-channel fluorescence images, with one channel used for identification of neurites and other channels for FISH.
circRNA Custom Code
By onCustom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.
Global Parkinson’s Genetics Program – Code
By onA centralized github repository for all code associated with the GP2 initative. This will be continually updated with new code as it gets developed.
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy
By onCode for analysis of multicolor fluorescence images to quantify fluorescence intensity at the perimeter of giant unilamellar vesicles (GUVs).
Code for making forest plots for top GWAS loci
By onThis repository contains the script used to create forest plots for top loci .
RHReynolds/neurodegen-psych-local-corr: Code to determine local and global genetic correlations between several neurodegenerative and neuropsychiatric disorders with LAVA and LDSC, respectively.
By onCode for paper "Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases" that explores local genetic correlations among neurodegenerative and neuropsychiatric diseases.
ensemblQueryR
By onA package allowing easy integration of Ensembl querying with a user’s R workflow.
Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
By onDetailed scripts to reproduce all analysis and data visualization for the paper "Integrated multi-cohort analysis of the Parkinson's disease gut metagenome."
