Macros and pipelines for analysis of image analysis
By savannah onImageJ 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
By savannah onScripts 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 ap) for analysis of total proteomes in response to nutrient stress
By savannah onWeb 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
By savannah onCode for extraction of any user-defined information from Uniprot.
Code for analysis of ER-phagy in iNeurons via proteomics
By savannah onCode for analysis of ER-phagy in iNeurons via proteomics. Associated with preprint: https://doi.org/10.1101/2023.06.26.546565
Long-read RNA seq analysis using Talon
By savannah onThis 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.
ensemblQueryR
By savannah onA package allowing easy integration of Ensembl querying with a user’s R workflow.
R code for paper Phenotype of GBA1 variants in individuals with and without Parkinson’s disease: The RAPSODI study
By savannah onThis 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”
By savannah onR Code used in "sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease."
Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
By savannah onDetailed 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.
Photometry analysis code
By savannah onThis Matlab script extracts GCaMP fiber photometry data and computes the number and amplitude of transients over time.
circRNA custom code
By savannah onCustom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.
Incentivized vigor task
By savannah onA 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.
twichma/Sequence-and-pattern-detection: Sequence and pattern detection code
By savannah onCode for sequence and pattern analyses.
Splicing-accuracy-manuscript
By savannah onCode for the splicing-accuracy manuscript (pre-print DOI to follow).
LiD genetic determinants study under CPH regression models
By savannah onCode to perform the study of LiD genetic determinants under CPH regression models and functional annotation analyses.
Neurite_FISH_Quant – Python code for quantification of FISH puncta in neurites
By savannah 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. The workflow assumes Z-stack, multi-channel fluorescence images, with one channel used for identification of neurites and other channels for FISH.
Single cell analysis of iPSC-derived midbrain organoids
By savannah 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.
katiekellyucl/W-PPI-NA-NSL-complex: v1.0.0. W-PPI-NA/NSL_complex
By savannah onSoftware for in Silico analysis linking the NSL complex to Parkinson’s disease and the mitochondria (protein-protein interaction data to functional enrichment analysis).