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.
R code for paper Phenotype of GBA1 variants in individuals with and without Parkinson disease: the RAPSODI study
By onThis is the R code used to produce the results described in the paper "Phenotype of GBA1 variants in individuals with and without Parkinson’s disease: The RAPSODI study"
Code for analysis of ER-phagy in iNeurons via proteomics
By onCode for analysis of ER-phagy in iNeurons via proteomics. Associated with preprint: https://doi.org/10.1101/2023.06.26.546565
Proband-NFL Analysis
By onCode used for the manuscript "Combining biomarkers for prognostic modelling of Parkinson’s disease" by Niro Viijaratnam and colleagues.
Code for splicing-accuracy-manuscript
By onCode used for manuscript: Splicing accuracy varies across human introns, tissues and age
AAV.CAP-Mac analysis code
By onFirst release of AAV.CAP-Mac analysis code and files to generate figures.
ImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections
By onImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections.
