Code Archive

The complete R-based Posit project reproduces the analyses and output in the article, "Population fraction of Parkinson's disease attributable to preventable risk factors."

The code provided here is the same "Supplementary Code" that is provided in the supplement of the manuscript. Individual level raw shotgun sequences and metadata are available on NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA834801.

Processed and normalized counts after the removal of low-quality genes and samples. These data are separated into colon ("colon_clean_VST_counts.csv") and brain ("brain_clean_VST_counts.csv"). The sample key can be found in the metadata at the GEO entry page. This repository contains the code that was used to generate these cleaned counts from the raw counts.

Code used in the analysis from the manuscript Wu et al., Investigation of the genetic aetiology of Lewy body diseases with and without dementia (2023).

A script to generate circular ROIs in each frame of a timelapse, using a previously generated track as reference. Used to measure fluorescence intensity (i.e., extracellular matrix content) along a microglia track. To be used as a continuation of 2_tracking.ijm.

A script to store in ImageJ’s ROImanager the tracks generated using Manual Tracking plugin, for later use (drawing tracks, frame-by-frame analysis). To be used as a continuation of 1_image_prep.ijm.

A script to register 2-channel timelapse images using HyperStackReg, using only 1 of the channels to compute transformation. The script also enhances contrast and prepares the image for manual tracking.

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.