Richert/Heterogeneous_SNNs: v1.0.0: Scripts to replicate the results of Gast et al. PNAS 2024
By onThis release includes configuration files and scripts to replicate the main results presented in Gast et al. PNAS 2024.
Direct visualisation of Alpha-Synuclein Oligomers in Human Brain
By onDirect visualisation of Alpha-Synuclein Oligomers in Human Brain
pyRASP
By onThe package "pyRASP" is a set of Python classes that can be run from scripts, interactive notebooks, and so on to analyze microscopy data. An example notebook is provided, showing user analyses.
3D printed MR-compatible stereotaxic frame for NHPs
By onA compact MRI-compatible stereotaxis suitable for a variety of NHP species (Macaca mulatta, Macaca fascicularis, and Cebus apella) that allows multimodal alignment through technique-specific fiducial markers.
Plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical and electrophysiological recordings
By onCode for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical (EChem) and electrophysiological (EPhys) recordings.
RNAseqProcessing
By onComparison of RNA QC tools trimmomatic and fastp. Additionally, scripts provided for RNA-seq processing steps, covering QC, alignment, and quantification.
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.
Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
By onThis repository contains analysis code for the publication found here, which explored the response of astrocytes, neurons and astro-neuronal co-cultures to alpha-synuclein oligomers.
R Code (RNA editing)
By onThe repository at https://github.com/karishdsa/ipscAstrNeurCocul contains single-cell and bulk RNA sequencing analysis of the cell culture models
Linear diffusion modeling of tau pathology spread
By onCode to reproduce all network analyses in Lubben et al. "LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread".
Fiber Photometry Data Analysis
By onCustom code for fiber photometry data pre-processing (bleaching correction, DF/F calculation, behavioral parsing...) are provided.
Script for the spike numbers in LRRK2 KI mice
By onThe script determines the number of spikes for each current injected step in the manuscript by Xenias et al. In addition, various parameters such as the threshold, maximum firing, rheobase, dy/dt, and FWHM are determined.
Single-cell-RNA-seq-of-the-CRISPR-engineered-endogenous-tauopathy-model
By onscRNA-seq data analysis workflow Step1: bash cellranger_mkfastq.sh This will generate fastq files. Step2: bash cellranger_count_submission.sh This will call another bash file “cellranger_count.sh” and generate count tables Step3: bash run_scrublet_multi.sh This will call “scrublet_multi.py” and generate scrublet results. If seeing error refer to “scrublet_multi_conditional.py”. Step4: bash scRNA_seq.sh This will call “seurat_individual.R” and generate QC plots for each sample. Step5: Run Rscript hassan_merged_seurat.r -l expectedCells/ -s scrublet/ -k outdir/ -j hassan2022 -r refdir path_to_ref_directory This will generate Seurat results. Step6: Proceed with the trajectory and the fly phone DB analysis, using their respective code, on the integrated Seurat object. Step7: pySCENIC Step8: OmicsIntegrator
Code for extracting FSCV spikes
By onCode for extracting FSCV spikes used in Amjad et al. 2024 10.1523/ENEURO.0001-24.2024.
Code for simulating FSCV artifacts
By onCode for simulating FSCV artifacts for algorithm validation in Amjad et al. 2024 10.1523/ENEURO.0001-24.2024
Automated spike sorter utilizing the super paramagnetic clustering algorithm.
By onTomSort is an automated spike sorter utilizing the superparamagnetic clustering (SPC) algorithm.
analysis codes related to “Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson’s disease model”
By onAnalysis codes related to "Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson’s disease model."
Refinement of efficient encodings of movement in the dorsolateral striatum throughout learning (CODE)
By onCustom MATLAB code was used to perform all the analyses contained within the research publication, "Refinement of efficient encodings of movement in the dorsolateral striatum throughout learning" by Jaidar and Albarran et al., 2024.
Code for Tang et al 2024
By onCode for Tang et al 2024 (https://doi.org/10.1038/s41586-023-06941-5) - https://doi.org/10.5281/zenodo.10146089
Astrocyte Editing
By onAnalysis code for studying astrocytes, neurons, and astro-neuronal co-cultures' response to alpha-synuclein oligomers is split between two repositories: on RNA sequencing, the other examines RNA editing in cell models and post-mortem brain samples.
