Analysis codes related to “Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson’s disease model”
By Emma Sherrell onAnalysis codes related to "Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson’s disease model."
Synapse function and gene enrichment analysis.
By Emma Sherrell onOnline tool for the exploration of snRNA sequencing dataset of dopamine neurons.
Code for extracting FSCV spikes
By Emma Sherrell onCode for extracting FSCV spikes used in Amjad et al. 2024.
Automated spike sorter utilizing the super paramagnetic clustering algorithm
By Emma Sherrell onTomSort is an automated spike sorter utilizing the super paramagnetic clustering (SPC) algorithm.
Single-cell-RNA-seq-of-the-CRISPR-engineered-endogenous-tauopathy-model
By savannah onscRNA-seq data analysis workflow.
Linear diffusion modeling of tau pathology spread
By savannah onCode to reproduce all network analyses in Lubben et al.: "LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread."
sCMOS calibration software
By Emma Sherrell onThis is software for calibrating sCMOS cameras, written in MATLAB. The readme file gives instructions on how to record experimental data and use the code to estimate the pixel-dependent offset, gain, variance, and read noise of a sCMOS camera.
R Code (RNA editing)
By Emma Sherrell onThe repository at https://github.com/karishdsa/ipscAstrNeurCocul contains single-cell and bulk RNA sequencing analysis of the cell culture models utilized in the study. This current repository contains the analysis of RNA editing in the cell culture models, as well as in a published dataset of post-mortem brain samples.
Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
By Emma Sherrell onThis current repository contains single-cell and bulk RNA-sequencing analysis of the cell culture models utilized in the study. The repository at https://github.com/aaronwagen/Astrocytes_editing contains the analysis of RNA editing in the cell culture models, as well as in a published dataset of post-mortem brain samples.
Script for the spike numbers in LRRK2 KI mice
By Emma Sherrell onThe script determines the number of spikes for each current injected step in the manuscript titled R1441C and G2019S LRRK2 knockin mice have distinct striatal molecular, physiological, and behavioral alterations by Xenias et al. In addition, various parameters such as the threshold, maximum firing, rheobase, dy/dt, and FWHM are determined.
Fiber photometry data analysis
By Emma Sherrell onCustom code for fiber photometry data pre-processing (bleaching correction, DF/F calculation, behavioral parsing...) are provided.
Plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical and electrophysiological recordings
By Emma Sherrell onCode for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical (EChem) and electrophysiological (EPhys) recordings.
Task data for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical and electrophysiological recordings
By Emma Sherrell onData for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical (EChem) and electrophysiological (EPhys) recordings.
3D printed MR-compatible stereotaxic frame for NHPs
By Emma Sherrell 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.
pyRASP
By Emma Sherrell onThe package "pyRASP" (written in support of https://www.biorxiv.org/content/10.1101/2023.12.18.572148v2) 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.
Richert/Heterogeneous_SNNs: v1.0.0: Scripts to replicate the results of Gast et al. PNAS 2024
By Julia Julia Leonard onThis release includes configuration files and scripts to replicate the main results presented in Gast et al. PNAS 2024, including Python scripts for the simulation, bifurcation analysis, and training of networks of Izhikevich neurons with heterogeneous spike thresholds.
RNAseq FASTQ: Effect of age and trisomy on transcriptional profile in cortex of Dp16 mice
By Emma Sherrell onCortex was isolated from control and Dp16 mice at 5 months of age and 14-16 months of age, and RNA was isolated and sequenced (5 mice per group, for a total of 20 mice).
ImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections
By savannah onImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections.
TX2P – Transcript to protein
By savannah onTX2P allows for automated integration of mass spectometry data in long-read RNA-sequencing workflow. It does so by predicting open reading frames for each transcripts within an input GTF/GFF file, translates it into peptide sequences and then searches for those predicted proteins in mass spec datasets using MetaMorpheus.