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."
LBD-case-case-GWAS
By onCode used in article: Investigation of the genetic aetiology of Lewy body diseases with and without dementia.
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
By onZenodo archive contains post-sequence QC, taxonomic, and functional profiling data. Supplementary Code includes workflow and bioinformatic processing used in the manuscript. Raw sequences and metadata are on NCBI SRA under BioProject ID PRJNA834801.
Population fraction of Parkinson’s disease attributable to preventable risk factors
By onR-based Posit project for replicating Parkinson's disease risk factor analysis. Includes data in 'input' folder, .Rproj file, renv lockfile, workflow scripts, and output scripts. Refer to README.md for more details.
