Code Archive

This 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. The workflow assumes Z-stack, multi-channel fluorescence images, with one channel used for identification of neurites and other channels for FISH.

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.

Software for in Silico analysis linking the NSL complex to Parkinson’s disease and the mitochondria (protein-protein interaction data to functional enrichment analysis).  

Python script for image analysis in Jensen et al., 2022.

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.  

This repository contains all the materials to build the mouse-reaching task and analyze the data acquired with this task.  

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 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.

Code for fMRI tasks designed to explore emotion-motor interactions—Active Escape and Approach-Avoidance tasks.

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.

This repository contains the script used to create forest plots for top loci .

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

An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis

Proband-NFL analysis

GUV quantification

Tutorials for HyDrop data analysis

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.