Code Archive

ImageJ macros and pipelines for analysis of pUb puncta, Keima Ratio, p62nuclei, and Parkin recruitment to mitochondria.

Scripts for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342

Web portal (shiney app) for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342

Code for extraction of any user-defined information from Uniprot.

Code for analysis of ER-phagy in iNeurons via proteomics. Associated with preprint: https://doi.org/10.1101/2023.06.26.546565

This is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) 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. It is forked from ANNSeq. The link includes the dag of the pipeline.

A package allowing easy integration of Ensembl querying with a user’s R workflow.

This is the R code used to produce the results described in the paper.

R Code used in "sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease."

Detailed scripts to reproduce all analysis and data visualization for the paper, "Integrated multi-cohort analysis of the Parkinson's disease gut metagenome," including an interactive shiny R app for exploration of metagenomic features of interest in the data sets.

This Matlab script extracts GCaMP fiber photometry data and computes the number and amplitude of transients over time.

Custom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.

A python program for a task in human participants using a joystick to make speeded reaches to cued targets. Also includes scripts for extracting behavioral variables, including kinematics.

Code for sequence and pattern analyses.

Code for the splicing-accuracy manuscript (pre-print DOI to follow).

Code to perform the study of LiD genetic determinants under CPH regression models and functional annotation analyses.

This 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.

The 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.

Software for in Silico analysis linking the NSL complex to Parkinson’s disease and the mitochondria (protein-protein interaction data to functional enrichment analysis).