Single cell analysis of iPSC-derived midbrain organoidson
The following script was used for analysis of gene corrected (GC) versus GBA1 mutant (MUT) midbrain organoids. The purpose was to combine, filter, integrate, and identify clusters and differentially expressed genes sets.
katiekellyucl/W-PPI-NA-NSL-complex: v1.0.0. W-PPI-NA/NSL_complexon
Software for in Silico analysis linking the NSL complex to Parkinson’s disease and the mitochondria (protein-protein interaction data to functional enrichment analysis).
Image analysis for Jensen et al., 2022on
Python script for image analysis in Jensen et al., 2022.
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons – DropSeqPipeline8on
This 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.
Mouse reaching taskon
This repository contains all the materials to build the mouse-reaching task and analyze the data acquired with this task.
Python script for Golgi cytoscape analysison
Custom Python script used for the cytoscape network analysis reported in doi.org/10.1101/2022.11.22.517583 (Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content).
Code used on the genetic determinants of early motor PD progression manuscript.
Python script used to generate the heatmap representation of identified LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308on
Python script used to generate the heatmap representation of identified high-confident LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308. It contains the data used for analysis as well as the necessary FASTA sequences for mapping of phosphosite positions on peptides to the original protein sequence.
fMRI tasks to explore emotion-motor interactionson
Code for fMRI tasks designed to explore emotion-motor interactions—Active Escape and Approach-Avoidance tasks.
Probedesign pipeline for the inhouse generation of seqFISH probeson
The probe design pipeline works by inputting the transcript id's for which probes have to be designed. Additional probe design parameters such as GC% or melting temperature can be changed via the config file. The pipeline will output the designed probes in fasta format and a csv file with the results of all filtering steps.
Code for making forest plots for top GWAS locion
This 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.on
Code for the paper: Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases: https://doi.org/10.1101/2022.05.30.22275781
Code used in the analysis from the manuscript Real et al., Association between the LRP1B and APOE loci and the development of Parkinson’s disease dementia (2022): https://doi.org/10.1101/2022.05.23.22275465
powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysison
An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Global Parkinson’s Genetics Program – Codeon
A suite of tools used by GP2 to analyze data.
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagyon
Tutorials for HyDrop data analysis
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysison
Power and sample size calculation for bulk tissue and single-cell eQTL analysis based on ANOVA, simple linear regression, or linear mixed-effects model. It can also calculate power/sample size for testing the association of an SNP to a continuous type phenotype.
Software for analyzing the expression of TEs at locus-specific resolutionon
TElocal takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements.