sPAtial Neuronal Gene Expression Atlas (PANGEA) Application
By onPANGEA is a web app for visualizing brain regional gene expression data. It's a spatial atlas showing gene patterns related to neurons vulnerable to α-synuclein pathology.
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
By onggtranscript simplifies visualizing transcript structure with new geoms like range(), intron(), junction(), and junction_label_repel(). It extends ggplot2's flexibility to create informative plots for publication.
katiekellyucl/W-PPI-NA-NSL-complex: v1.0.0. W-PPI-NA/NSL_complex
By onSoftware for in Silico analysis linking the NSL complex to Parkinson’s disease and the mitochondria (protein-protein interaction data to functional enrichment analysis)
powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
By onEasy-to-use web application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Manual Tracking/image_prep.ijm
By 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.
Manual Tracking/tracking.ijm
By 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/measure_ECM.ijm
By 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. .
Video tutorials for Curtain and Curtain-PTM
By onVideo tutorials to assist users of Curtain and Curtain-PTM proteomic data analysis web tools (described in ).
State-dependent GABAergic regulation of striatal spiny projection neuron excitability: NEURON + Python model of striatal projection neurons
By 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 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. The main purpose of the software is to provide a tool that allows for the implementation of biologically informed spiking neural networks and optimize the parameters of these networks via gradient descent. As such, RectiPy can be used to optimize a spiking network model of the basal ganglia to fit neural activity recordings, for example. RectiPy provides an intuitive YAML interface for model definition, and leverages PyRates to translate these model definitions into PyTorch functions. This way, users can easily define their own neuron models, spike-based or rate-based, and use them to create a RNN model. All model training, testing, as well as numerical integration of the differential equations is also performed in PyTorch. Thus, RectiPy comes with all the gradient-based optimization and parallelization features that PyTorch provides. RectiPy is freely available at https://github.com/pyrates-neuroscience/RectiPy and comes with a full online documentation and various use examples:
Reward perseveration is shaped by GABAA-mediated dopamine pauses: Software
By onCode provided for data analysis and figure generation in the paper "Reward perseveration is influenced by GABAA-mediated dopamine pauses".
ASAP CRN Cloud GitHub
By onThis GitHub repository, maintained by DataTecnica and DNAstack, includes the curation methodology and code for the harmonization of ASAP CRN Cloud data.
Synapse Quantification with Puncta Analyzer
By onProtocol for installing and using Puncta analyzer for synapse image analysis
ilastik install and run for Syn Bot (Windows Version)
By onVideo tutorials available for installing, training, and using ilastik project on Windows for SynBot
ilastik install and run for Syn Bot (Mac Version)
By onVideo guide for installing, training, and using ilastik project on Mac for SynBot run.
Installing FIJI and SynBot (Windows Version)
By onVideo tutorial for installing FIJI and SynBot on Windows OS, along with a demonstration of a basic SynBot run.
Software for data analysis used in the manuscript “Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinson’s disease” (doi: 10.1073/pnas.2402206121)
By onSeurat version 3 was used for single-cell analysis, applying quality control steps to remove outliers and potential multiplets. Scripts and data are available on Dryad (https://doi.org/10.5061/dryad.pk0p2ngvp).
manuelatan/PD-survival-GWAS: Release 2.0
By onCode used for PD progression survival GWAS to mortality, and Hoehn and Yahr stage 3 or greater (H&Y3+).
Analytical Tool for spatial gene expression with 10x Visium Platform
By onAn analytical tool to be used with the 10X Visium platform to compare spatial gene expression values.
Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology Code: Goralsth/Spatial-transcriptomicSpatial transcriptomics Code: Spatial-transcriptomics-reveals-molecular-dysfunction-associated-with-cortical-Lewy-pathology
By onCode repository for Goralski, et., al., 2024.