scAlleleExpression: R package for downstream analysis of allele specific expression single cell data
By onAn R package for investigating Cell Type specific regulatory genetics using single cell or nuclei allele specific expression data. It loads ASE pipeline output, performs ASE analysis, and works with various ASE pipelines.
scASE_py: Python pacakge for loading single cell allele specific data
By onPython package for single cell allele-specific expression (ASE) output manipulation available at https://github.com/seanken/ASE_pipeline. R package for downstream analysis at https://github.com/seanken/scAlleleExpression.
CellLevel_QC: Extracting cell level QC metrics from CellRanger barcoded bams
By onJava code in this repository retrieves cell level mapping data (intronic reads, intergenic reads, multimapped reads, etc) from CellRanger output. Compatible with CellRanger v5 and v6, may work with newer versions and Spaceranger output.
Single cell allele specific expression processing pipeline for long read data
By onPipeline processes long read single cell/nucleus 10X data (ONT, PacBio, MAS-Seq) to generate gene/isoform-level allele-specific expression (ASE) counts.
Analyses of metabolite profiling of Drosophila Parkinson’s Disease model for identifying novel glial-based therapeutic targets
By onGenetic screening and metabolomics show glial adenosine metabolism as a potential treatment for Parkinson’s disease. Analysis includes measuring metabolite levels in synuclein expressing/control fly brains with different methods.
HYX990205/ReRx: Drug Repurposing for Parkinson’s Disease
By onToolkit for drug repurposing analysis used in the preprint: "Drug Repurposing for Parkinson's Disease: A Large-Scale Multi-Cohort Study" Find more at https://doi.org/10.1101/2025.05.20.25327943.
SIFT based MATLAB script [Hanna et al 2024]
By onSIFT based MATLAB script used in the preprint Hanna et al 2024
Python code: Figure generating script [Hanna et al 2024]
By onPython code: Figure generating script used in the preprint Hanna et al 2024
ImageJ code: Analysis script_0 [Hanna et al 2024]
By onImageJ code: Analysis script_0 used in the preprint Hanna et al 2024
Script for image quantification [Wang et al 2025]
By onScript for image quantification used in Wang et al 2025
Version 1.0 Neuromelanin quantification R scripts
By onVersion 1.0 release of Neuromelanin quantification R scripts
Collection of command-line Python-based scripts for voxel-wise computation
By onCollection of command-line Python-based scripts for voxel-wise computation
Script for rat brain images processing
By onScript for rat brain images processing used in https://doi.org/10.1101/2024.10.22.619619
Custom Phyton scripts related to Bouabid, S. et al (2025) “Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations””
By onPhyton scripts written by Safa Bouabid and adapted from Han Lab for reading 2D treadmill ball velocity with Raspberry Pi.
Custom MATLAB scripts related to Bouabid, S. et al. (2025) “Distinct spatially organized striatum-wide acetylcholine dynamics for the learning and extinction of Pavlovian associations”
By onMATLAB scripts written by Safa Bouabid to analyse ACh release dynamics, DA release, glutamate release onto cholinergic interneurons, and behavioural changes in mouse striatum during learning and extinction of Pavlovian associations.
Custom scripts related to Graziano, M. et al. (2025) “A molecular atlas of cell-type specific signatures in the parkinsonian striatum”
By onScripts by Graziano and Masarapu aid in analyzing single-nucleus RNA sequencing data from Parkinson's Disease striatum, mapping vulnerabilities, and inferring cell trajectories. Giacomello Lab scripts are available on GitHub.
Code used in “Lrrk2 G2019S mutation incites increased cell-intrinsic neutrophil effector functions and intestinal inflammation in a model of infectious colitis”
By onUsing scRNAseq and flow cytometry, we demonstrated that the Lrrk2-G2019S mutation is associated with an increased neutrophil presence in the colonic lamina propria, Th17 skewing, upregulated Il17a, and greater colonic pathology during infection.
Tailored workflows for the analysis of transposable elements (Garza et al, 2025)
By onGarza et al. (2025) created customized workflows for transposable element analysis across various data types. Workflows are in Snakemake, Jupyter notebooks, R markdowns, and scripts. Details are in the GitHub README.
R Code used in “Sex-Specific Microglial Responses to Glucocerebrosidase Inhibition: Relevance to GBA1-Linked Parkinson’s Disease”
By onR Code used in "sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease."
LiD genetic determinants study under CPH regression models
By onCode to perform the study of LiD genetic determinants under CPH regression models and functional annotation analyses.
