Neurite_FISH_Quant–Python code for quantification of FISH puncta in neurites
By 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, as specified below. The workflow assumes Z-stack, multi-channel fluorescence images, with one channel used for identification of neurites and other channels for FISH.
circRNA Custom Code
By onCustom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.
Global Parkinson’s Genetics Program – Code
By onA centralized github repository for all code associated with the GP2 initative. This will be continually updated with new code as it gets developed.
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy
By onCode for analysis of multicolor fluorescence images to quantify fluorescence intensity at the perimeter of giant unilamellar vesicles (GUVs).
Code for making forest plots for top GWAS loci
By 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 onCode for paper "Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases" that explores local genetic correlations among neurodegenerative and neuropsychiatric diseases.
ensemblQueryR
By onA package allowing easy integration of Ensembl querying with a user’s R workflow.
Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
By onDetailed scripts to reproduce all analysis and data visualization for the paper "Integrated multi-cohort analysis of the Parkinson's disease gut metagenome."
Mouse reaching task
By onThe repository includes materials for building and analyzing data from a mouse-reaching task: a bill of materials, 3D models, schematics, an Arduino controller, video recording scripts, and data analysis scripts using DLC.
fMRI tasks to explore emotion-motor interactions
By onCode for fMRI tasks designed to explore emotion-motor interactions—Active Escape and Approach-Avoidance tasks in the Socal Kinesia and Incentivization for Parkinson's Disease (SKIP) dataset.
Python script for Golgi cytoscape analysis
By 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).
Photometry Analysis Code
By onThis set of functions extracts GCaMP Fiber Photometry data obtained with a TDT system, performs isosbestic and exponential correction, and computes the number and amplitude of transients over time. The code was originally used for the following experiment: MFB-lesioned 6-OHDA D1-cre or A2A-cre mice were injected with a cre-dependent GCaMP6f in dorsolateral striatum and implanted with 400um optical fibers. Mice were placed in an open field arena and recorded for 30 minutes before levodopa injection, and 120 minutes after levodopa injection. The experiment includes video from 2 cameras and a TTL pulse from an Arduino indicating the time when levodopa was injected.
Incentivized Vigor Task
By onCode for an fMRI task in which human participants use a joystick to make speeded reaches to cued targets. This task examines incentive effects on movement, part of the Socal Kinesia and Incentivization for Parkinson's Disease (SKIP) dataset.
Code for extraction of any user-defined information from uniprot
By onCode for extraction of any user-defined information from Uniprot.
twichma/Sequence-and-pattern-detection: Sequence and pattern detection code
By onThe code provided is for analyzing sequences and patterns.
Macros and pipelines for analysis of image analysis
By onImageJ macros and pipelines for analysis of pUb puncta, Keima Ratio, p62nuclei and Parkin recruitment to mitochondria.
Evaluation of a novel method for spectral analysis of neurophysiology data
By onThis code implements a novel method for correcting a distortion effect that is present in the power spectra of neuronal spike trains.
Software for analyzing the expression of TEs at locus-specific resolution
By onWe enable the locus-specific analysis of transposable elements, with curated GTF files to improve detection of yound transposable elements, such as HERVs and young L1s. Parts of this software will be used for single-cell TE anlaysis protocols, which are under development
R scripts for analysis of publication “Sex distribution of GBA1 Variants Carriers with Dementia with Lewy Bodies and Parkinson Disease”
By onR scripts for analysis of publication "Sex distribution of GBA1 variant carriers with dementia with Lewy Bodies and Parkinson's disease."
