Code for analysis of smell test dataset included in: Development of a Simplified Smell Test to Identify Patients with Typical Parkinson’s as Informed by Multiple Cohorts, Machine Learning and External Validation
By Emma Sherrell onCode used for the analysis of smell test performance as reported in "Development of a Simplified Smell Test to Identify Patients with Typical Parkinson’s as Informed by Multiple Cohorts, Machine Learning and External Validation," Li et al., 2024.
Scripts for snRNAseq data analysis
By Emma Sherrell onScripts for analyzing single nuclei sequencing data from healthy and Parkinson's disease brains include creating a reference database with transposable element annotations and a file for Cell Ranger to produce snRNA count matrices.
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 Emma Sherrell 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).
scNAT Data for “scNAT: A deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles”
By Emma Sherrell onData for "scNAT: A deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles" publication.
CNV calling pipeline for low coverage single-cell whole genome sequencing data
By Emma Sherrell onPipeline for analyzing, filtering, and comparing copy number variations from single-cell whole genome sequencing data that were amplified using PicoPLEX, PTA, or droplet MDA.
egustavsson / GBA_GBAP1_manuscript
By savannah onCode used to generate the plots used in manuscript, "The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1" (DOI: 10.1126/sciadv.adk1296).
FIJI Syn_Bot Macro
By savannah onAt a neuronal synapse, presynaptic and postsynaptic terminals are ~50nm apart, and thus immunohistochemical staining of a protein from each compartment will give a colocalized signal due to the resolution limits of traditional fluorescence microscopy. This macro counts the number of colocalized synaptic puncta in fluorescence microscopy images.
SNCA transcript diversity in neurons
By savannah onThis repository contains the code used to generate the plots used in the SNCA transcript expression and ASO modulation manuscript.
Synapse quantification with Puncta Analyzer
By savannah onProtocol for installing Puncta Analyzer and using it to analyze synapse images.
ilastik install and run for Syn Bot (Windows version)
By savannah onVideo instructions for installing ilastik, training an ilastik project, and using the ilastik project for simple SynBot run for Windows operating system.
ilastik install and run for Syn Bot (Mac version)
By savannah onVideo instructions for installing ilastik, training an ilastik project, and using the ilastik project for simple SynBot run for Mac operating system.
Installing FIJI and SynBot (Windows version)
By savannah onVideo instructions for installing FIJI and SynBot and a simple SynBot run for Windows operating system.
ASAP CRN Cloud GitHub
By savannah onThis GitHub repository, maintained by DataTecnica and DNAstack, includes the curation methodology and code for the harmonization of ASAP CRN Cloud data.
Code for Tang et al., 2024
By savannah onCode for Tang et al., 2024 (https://doi.org/10.1038/s41586-023-06941-5) - https://doi.org/10.5281/zenodo.10146089.
Refinement of efficient encodings of movement in the dorsolateral striatum throughout learning (CODE)
By savannah 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.
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.
