Ephys data analysis

a very small segment of scripts used during my PhD in McNaughton Lab

1. AnalysisJustinVR: different scripts used to analyze VR data from hippocapus and visual cortex
2. BehaviorTracking: markerless open-field tracking of mouse using DeepLabCut (http://www.mackenziemathislab.org/deeplabcut)
3. CG_Monosyn: compute auto-correlogram, cross-correlogram and monosynaptic connections between neurons using CellExplorer (https://cellexplorer.org/)
4. IntanCorrTests: intan correlation test for checking shorts
5. PVanalysis: compute population sparsity, PCA scree plot, raster map embedding, low-d manifold (https://github.com/MouseLand/rastermap)
6. SequenceAnalysis: theta sequence decoding + reactivation strength using PCA
7. kc_analysis: k-complex detection script
8. placecelldecoding: bayesian decoding using maximum-likelihood approach (https://pubmed.ncbi.nlm.nih.gov/8036517/)
9. postEphysSorting: post kilosort processing based on Allen Institute metrics (add link)
10. ripple_analysis: sharp-wave ripple detection script
11. up-down states: up-states detection script
12. PCA trajectory plots

To-Do

always things to do ;)