Neurite_FISH_Quant – Python code for quantification of FISH puncta in neurites
By savannah 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. The workflow assumes Z-stack, multi-channel fluorescence images, with one channel used for identification of neurites and other channels for FISH.
Single cell analysis of iPSC-derived midbrain organoids
By savannah onThe 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_complex
By savannah onSoftware 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., 2022
By savannah onPython script for image analysis in Jensen et al., 2022.
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons – DropSeqPipeline8
By savannah 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.
Mouse reaching task
By savannah onThis repository contains all the materials to build the mouse-reaching task and analyze the data acquired with this task.
Python script for Golgi cytoscape analysis
By savannah onCustom 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).
Python script used to generate the heatmap representation of identified LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308
By quincy.tichenor onPython 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 interactions
By quincy.tichenor onCode for fMRI tasks designed to explore emotion-motor interactions—Active Escape and Approach-Avoidance tasks.
Probedesign pipeline for the inhouse generation of seqFISH probes
By taliag onThe 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 loci
By quincy.tichenor 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 Blythe Lloyd onCode for the paper: Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases: https://doi.org/10.1101/2022.05.30.22275781
huw-morris-lab/PDD_GWSS
By Blythe Lloyd onCode 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 analysis
By taliag onAn R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Global Parkinson’s Genetics Program – Code
By Blythe Lloyd onA suite of tools used by GP2 to analyze data.
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy
By taliag onGUV quantification
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
By Blythe Lloyd onPower 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.