Code for clinical dataset analysis included in: Persistent Hyposmia as Surrogate for α-Synuclein-Linked Brain Pathology
By onCode used for the analysis of clinical data as reported in the study "Persistent Hyposmia as Surrogate for α-Synuclein-Linked Brain Pathology" in Mollenhauer, Li et al., MedRxiv 2023
Code for analysis of smell test dataset included in: Development of a Simplified Smell Test to Identify Patients with Typical Parkinson’s as Informed by Multiple Cohorts, Machine Learning and External Validation
By onCode used for the analysis of smell test performance as reported in "Development of a Simplified Smell Test to Identify Patients with Typical Parkinson’s as Informed by Multiple Cohorts, Machine Learning and External Validation", Li et al., 2024
Nextflow pipeline for Nanopore WGS analysis
By onNextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.
CREsted (Cis-Regulatory Element Sequence Training, Explanation and Design): a deep learning package for training enhancer models on single-cell ATAC sequencing (scATAC-seq) data
By onCREsted offers detailed analyses and tutorials for studying enhancer codes and creating synthetic enhancer sequences at cell type-specific, nucleotide-level resolution.
HA_Skeleton_Analysis
By onThis script assesses the complexity of extracellular matrix network through a skeleton analysis
Directionality_GMX
By onThis script calculates a directionality index to assess the randomness of cell movement
Analyses of metabolite profiling of Drosophila Parkinson’s Disease model for identifying novel glial-based therapeutic targets
By onGenetic screening and metabolomics show glial adenosine metabolism as a potential treatment for Parkinson’s disease. Analysis includes measuring metabolite levels in synuclein expressing/control fly brains with different methods.
R scripts for the statistical analysis and ploting in the paper GEARBOCS: An Adeno Associated Virus Tool for In Vivo Gene Editing in Astrocytes
By onR scripts for the statistical analysis and plotting in the paper GEARBOCS: An Adeno Associated Virus Tool for In Vivo Gene Editing in Astrocytes
Peripheral Immune Neurodegeneration
By onProject investigates if immune cells impact neurodegenerative diseases differently based on ancestry. It examines disease gene expression and genetic links in African, East Asian, and European populations.
POLCAM-SR: Version 1.4
By onSoftware for processing single-molecule and diffraction limited polarisation camera image data.
RoSE-O_POLCAM
By onRoSE-O adapted for SMOLM using polarization camera. Can also be modified to work with other single-channel imaging systems.
Preprocessing pipeline to establish and extract data from ROIs from multifiber photometry movies
By onPipeline and code are available for imaging data preprocessing using a micro-fiber array approach to measure and manipulate local dynamics in mice, allowing study of cell-specific signals in 3-D volumes.
Custom G-code used to jet-print microfluid-walled dumbbells
By onAll original G-code used to jet-print the microfluid-walled dumbbells described in Nebuloni, F. et al. (2024) study.
R scripts associated with SpatialBrain.org
By onAll original R code written to analyse results shown in SpatialBrain.org and Kilfeather & Koo et al. (2024) "Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease".
Pipeline and MATLAB scripts for micro-CT-based fiber localization
By onPipeline and MATLAB script for micro-CT-based method for precise fiber localization and atlas alignment after performing micro-fiber photometry in behaving mice.
Code for: Dissociation of putative open loop circuit from ventral putamen to motor cortical areas in humans I: high-resolution connectomics
By onCode for pre-processing fMRI data and region on interest masks associated with Rixor et al. 2024.
Outlier waveform detection for internal globus pallidus (GPi) activity
By onMatlab code identifies single units with spike waveforms that take on outlier feature values in the internal segment of the globus pallidus (GPi) units recorded from two nonhuman primates (in healthy and parkinsonian states).
