suny-downstate-medical-center/pd_m1_6ohda: M1_Control_6OHDA
By onLiqiang Chu et al found decreased excitability in these neurons in a Parkinson's mouse model. A simulation using NetPyNE was created to study the impact of the changed PT5B neuron on motor cortex spiking dynamics.
Matlab code: Determination of precisely timed sequences of calcium events
By onThe file "Identify_sequences.m' used to identify sequences of calcium imaging events.
Matlab code: Event-based analysis of calcium transients
By onMatlab algorithms to align raw calcium traces to behavioral events during a behavioral task.
TRAP In Vivo Analysis
By onGitHub Code and data from Ryan et al., 2024. Includes TRAP_InVivo_Analysis.m for Plexon MAP data analysis, TRAP_Remove_INs.m for removing putative interneurons, and Summary.mat containing behavior/electrophysiology data used for Figures 1 and S1.
TRAP-Rabies-Analysis
By onStudy by Ryan et al., 2024 used mice injected with viruses to label neurons in the brain. Resource is GitHub code with Rabies_Analysis.m to analyze data to map neurons and Rabies_Summary.mat contains normalized data for figures 2 and S2.
Open Field Analysis
By onA Python script processes open field analysis data from an excel sheet to calculate average velocity,rotations, and distance moved. The output is stored in a 'Metrics' spreadsheet, cross-checked with manually computed metrics in another sheet.
Code-Sheng et al 2025
By onCustom Matlab and Labview code used in analysis in Sheng et al 2025 paper.
nix-lir-binding-to-wipi2d
By onScripts used to analyze molecular dynamics simulations of NIX bound to WIPI2d in the following publication: https://doi.org/10.1101/2024.08.28.609967
Calcium and Behavior Video Alignment Scripts for Open-Field Dyskinesia Analysis (Alcacer et al., Cell Reports 2025)
By onMatlab scripts for alignment of calcium imaging videos and videos from mice in an open field arena recorded from a bottom camera from Alcacer et al. 2025.
Custom MATLAB scripts related to Zhang, Y. et al (2025) “An axonal brake on striatal dopamine output by cholinergic interneurons”
By onMATLAB scripts written by Yan-Feng Zhang to predict how nicotinic receptors impact on dopamine transient in vivo during the dynamic tonic and multiphasic activity in cholinergic interneurons.
Baseline α–synuclein Seeding Activity and Disease Progression Code
By onThe project analyzes baseline α-synuclein seeding activity and Parkinson's disease progression.
SNr subpopulation neuroanatomy-code
By onMatlab scripts used to plot anatomical data related to the study: Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses.
R Code used in “Sex-Specific Microglial Responses to Glucocerebrosidase Inhibition: Relevance to GBA1-Linked Parkinson’s Disease”
By onR Code used in "sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease."
LiD genetic determinants study under CPH regression models
By onCode to perform the study of LiD genetic determinants under CPH regression models and functional annotation analyses.
Single cell analysis of iPSC-derived midbrain organoids
By 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. This is part of a Collection of protocols (dx.doi.org/10.17504/protocols.io.8epv593dng1b/v1) for the paper "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" (https://doi.org/10.21203/rs.3.rs-1521848/v1)
huw-morris-lab/PDD_GWSS
By onThe manuscript by Real et al. investigates the relationship between LRP1B and APOE loci and the onset of Parkinson’s disease dementia, utilizing specific code for analysis.
Long-read RNA seq analysis using Talon
By onThis is a pipeline that takes fastq data as input, generates fastq stats using nanostat, performs fastq processing and filtering using pychopper, maps the reads to the genome using minimap2, and uses talon to assemble and quantify transcripts.
Probedesign pipeline for the inhouse generation of seqFISH probes
By onThe probe design pipeline works by inputting the transcript id's for probes to be designed. The pipeline will output the designed probes in fasta format and a csv file with the results of all filtering steps.
