Code Archive

scRNA-seq data analysis workflow.

Code to reproduce all network analyses in Lubben et al.: "LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread."

This 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.

The 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.

This 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.

The 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.

Custom code for fiber photometry data pre-processing (bleaching correction, DF/F calculation, behavioral parsing...) are provided.

Code for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical (EChem) and electrophysiological (EPhys) recordings.

Data for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical (EChem) and electrophysiological (EPhys) recordings.

A 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.

The 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.

This 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.

Cortex 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.

TX2P 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.

This repository contains a NEURON + Python model of striatal projection neurons (or SPNs) designed to simulate the interaction between GABAergic and glutamatergic synaptic inputs.

Recurrent neural network training in Python (RectiPy) is a software package developed by Richard Gast that allows for lightweight implementations of recurrent neural networks (RNNs) based on ordinary or delayed differential equations. Here, the team provides a tool that allows for the implementation of biologically informed spiking neural networks and optimizes the parameters of these networks via gradient descent.

This repository contains five Jupyter Notebooks (Python 3.0) created or modified for specific use with action potential analysis for the Zampese, et.al. 2022 Science Advances paper.

This script and accompanying folder containing *.csv files of data should reproduce figures 1-4 and supplementary figure S1 of the manuscript in GABAergic regulation of striatal spiny projection neuron excitability depends upon their activity state (2023).

This code implements a novel method for correcting a distortion effect that is present in the power spectra of neuronal spike trains. This method is compared to an alternative, inter-spike interval shuffling procedure that has been conventionally employed for this purpose in the past.