In vivo and in silico alpha-synuclein propagation dynamics: The role of genotype, epicentre, and connectivity

This repository contains the source data and code for the analyses in the manuscript titled "In vivo and in silico alpha-synuclein propagation dynamics: The role of genotype, epicentre, and connectivity" Main subject file csv: masterfile-timepoint-data.csv however two additional csv files used for analysis are as following: behaviour-trial-data.csv -- data structured by trial to enable cox analysis symptom-and-survival-tracking-data.csv -- symptom tracking and survival information provided separately since experimenter S.T. was blind to genotype and injection group All *.R files are R code scripts and named according to the analysis performed Behavioural analyses survival_and_symptom_profile.R weight-RRbehaviour.R PT-cox-analysis.R WH-cox-analysis.R Deformation-based analysis: voxel-wise volume trajectories for CP injection: DBM-models-and-peak-voxel-plots.R for DG injection: hippocampal-injection-experiment-DBM.R DBM outputs: for CP injection experiment: striatum-DBM-template.mnc striatum-DBM-template-mask.mnc for DG injection experiment: hipp-DBM-template.mnc hipp-DBM-template-mask.mnc SIR computational modelling analysis script: abm-mouse-withatrophy.py; original script: https://github.com/srahayel/SIR_mouse improved upon code to include measurements of atrophy, inspired by https://github.com/yingqiuz/SIR_simulator SIR simulated vs empirical atrophy analysis SIR_CP-seed_analysis.R with accompanying empirical atrophy measures: CP-empirical-atrophy.csv SIR_DG-seed_analysis-max.R with accompanying empirical atrophy measures: DG-empirical-atrophy.csv other important csv files that help with this analysis: simulated atrophy (output from SIR python script: CP seed: abm_spread_v.425.0.spread_rate.0.01.dt.0.1.seed.35.injection_amount.2.5e-06.clearance_gene.None.k1.0.9.k2.0.9.csv DG seed: abm_spread_v.730.0.spread_rate.0.07.dt.0.1.seed.40.injection_amount.2.5e-06.clearance_gene.None.k1.0.9.k2.0.9.csv AMBA-acronym-labels-for-plotting.csv AMBA-region-labelnumbers-withacronyms.csv AMBA-region-labelnumbers.csv connectivity-strength-AMBCA.csv SNCA-gene-expression-AMBA.csv