State-dependent GABAergic regulation of striatal spiny projection neuron excitability: NEURON + Python model of striatal projection neurons
By Emma Sherrell onThis repository contains a NEURON + Python model of striatal projection neurons (or SPNs) designed to simulate the interaction between GABAergic and glutamatergic synaptic inputs.
RectiPy software package
By Emma Sherrell onRecurrent 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.
surmeierlab/EZT2022SA: EZTNotebooks
By Emma Sherrell onThis 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.
Day2024 R code and analysis
By Emma Sherrell onThis 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).
Evaluation of a novel method for spectral analysis of neurophysiology data
By Emma Sherrell onThis 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.
Population fraction of Parkinson’s disease attributable to preventable risk factors
By Emma Sherrell onThe complete R-based Posit project reproduces the analyses and output in the article, "Population fraction of Parkinson's disease attributable to preventable risk factors."
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
By Emma Sherrell onThe code provided here is the same "Supplementary Code" that is provided in the supplement of the manuscript. Individual level raw shotgun sequences and metadata are available on NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA834801.
Boles_et-al_DSS_time-series
By Emma Sherrell onProcessed and normalized counts after the removal of low-quality genes and samples. These data are separated into colon ("colon_clean_VST_counts.csv") and brain ("brain_clean_VST_counts.csv"). The sample key can be found in the metadata at the GEO entry page. This repository contains the code that was used to generate these cleaned counts from the raw counts.
LBD-case-case-GWAS
By Emma Sherrell onCode used in the analysis from the manuscript Wu et al., Investigation of the genetic aetiology of Lewy body diseases with and without dementia (2023).
Manual Tracking/measure_ECM.ijm
By savannah onA script to generate circular ROIs in each frame of a timelapse, using a previously generated track as reference. Used to measure fluorescence intensity (i.e., extracellular matrix content) along a microglia track. To be used as a continuation of 2_tracking.ijm.
Manual Tracking/tracking.ijm
By savannah onA script to store in ImageJ’s ROImanager the tracks generated using Manual Tracking plugin, for later use (drawing tracks, frame-by-frame analysis). To be used as a continuation of 1_image_prep.ijm.
Manual Tracking/image_prep.ijm
By savannah onA script to register 2-channel timelapse images using HyperStackReg, using only 1 of the channels to compute transformation. The script also enhances contrast and prepares the image for manual tracking.
Macros and pipelines for analysis of image analysis
By savannah onImageJ macros and pipelines for analysis of pUb puncta, Keima Ratio, p62nuclei, and Parkin recruitment to mitochondria.
Scripts for analysis of total proteomes in response to nutrient stress
By savannah onScripts for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Web portal (shiney ap) for analysis of total proteomes in response to nutrient stress
By savannah onWeb portal (shiney app) for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Code for extraction of any user-defined information from uniprot
By savannah onCode for extraction of any user-defined information from Uniprot.
Code for analysis of ER-phagy in iNeurons via proteomics
By savannah onCode for analysis of ER-phagy in iNeurons via proteomics. Associated with preprint: https://doi.org/10.1101/2023.06.26.546565
Long-read RNA seq analysis using Talon
By savannah onThis is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) 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. It is forked from ANNSeq. The link includes the dag of the pipeline.
ensemblQueryR
By savannah onA package allowing easy integration of Ensembl querying with a user’s R workflow.
R code for paper Phenotype of GBA1 variants in individuals with and without Parkinson’s disease: The RAPSODI study
By savannah onThis is the R code used to produce the results described in the paper.