Code for Murray et al. 2026 (Prolonged Timescales) Manuscript
By onSource code to replicate core analyses used throughout the Murray et al. 2026 (Prolonged Timescales) manuscript.
Data and code for Stasiak et al. 2026 (TREV-Emotion) Manuscript
By onOnline repository for the data and scripts used in the Stasiak et al., 2026 preprint on TREV-derived cardiac contractility in threat anticipation contexts.
FushikiA_etal_2024: PD Model Mice Study – v1.0 Code
By onRepository offers tools for processing, analyzing, and visualizing data related to PD and dopaminergic neurons.
Code for Miller-Hansen article “Thalamus orchestrates local acetylcholine-dependent dopamine release in the learning striatum”
By onThis is the code generated by Miller-Hansen for analyzing output from Guppy.
Mathematica code for Astrocytes mediate the dopaminergic modulation of tonic GABAergic signaling in substantia nigra
By onMathematica notebook containing functions used to measure spikerates, draw histograms, and extract current traces from Clampfit raw data exports.
Code used to analyze striatum population dynamics during isometric forelimb actions
By onCode used for analysis and figures for paper titled: "Striatal ensembles specify and control granular forelimb actions".
TEsingle pipeline for analysis of Martirosyan dataset
By onCode to analyze Martirosyan et al. substantia nigra single nuclei RNA-seq dataset with TEsingle.
TEsingle benchmarking pipeline
By onCode to perform benchmarking of simulated single cell/nuclei RNA-seq datasets with TEsingle and other scRNA-seq software.
Cactus
By onCactus (10.5281/zenodo.7351087) manages session data for curtain and curtainptm backends, handling saving and loading operations efficiently.
VariantAnalysis: Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease
By onIntegrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease
Code – bulkRNA-seq data from WT, ATP13A2 c.1306
By onCode - bulkRNA-seq data from WT, ATP13A2 c.1306 related to "ATP13A2 Loss of Function-Driven Polyamine Dysregulation Induces SAM Depletion and Epigenetic Astrocyte Toxicity"
bisulfite sequencing
By onbisulfite sequencing related to "ATP13A2 Loss of Function-Driven Polyamine Dysregulation Induces SAM Depletion and Epigenetic Astrocyte Toxicity"
bulkATAC-seq data from WT, ATP13A2 c.1306
By onbulkATAC-seq data from WT, ATP13A2 c.1306 related to "ATP13A2 Loss of Function-Driven Polyamine Dysregulation Induces SAM Depletion and Epigenetic Astrocyte Toxicity"
Mitochondrial Proteostasis Cryo-ET Analysis
By onCollection of scripts used for the analysis of cryo-ET data in Ehses et al., 2026. The code, written in MATLAB 2019b, includes pipelines for tomogram pre-processing and reconstruction as well as particle quantification.
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.
Single cell analysis of iPSC-derived midbrain organoids
By 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. This is part of a Collection of protocols (dx.doi.org/10.17504/protocols.io.8epv593dng1b/v1) for the paper "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" (https://doi.org/10.21203/rs.3.rs-1521848/v1)
huw-morris-lab/PDD_GWSS
By onThe manuscript by Real et al. investigates the relationship between LRP1B and APOE loci and the onset of Parkinson’s disease dementia, utilizing specific code for analysis.
Long-read RNA seq analysis using Talon
By onThis is a pipeline that takes fastq data 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.
Probedesign pipeline for the inhouse generation of seqFISH probes
By onThe probe design pipeline works by inputting the transcript id's for probes to be designed. The pipeline will output the designed probes in fasta format and a csv file with the results of all filtering steps.
