mukhes3/ampad_lineage

Ordering patients on smooth manifolds using lineage estimation tools

AMPAD_Lineage

Ordering patients on smooth manifolds using lineage estimation tools

Code to generate Monocle data structure

TCX_GenerateMonocleDS.R (DE genes)

DLPFC_GenerateMonocleDS.R (DE genes)

TCX_DE_PStime_HighVar.R (High variance genes)

DLPFC_DE_PStime_HighVar.R (High variance genes)

Code to plot fraction of AD as a function of pseudotime

TCX_FractionAD_vs_PS.R

DLPFC_FractionAD_vs_PS.R

Code to plot cell type specific marker expression as a function of pseudotime (and calculate p-value)

CellTypeMarkerExpression_TCX.R

CellTypeMarkerExpression_DLPFC.R

Code to make box plots and lineage plots

TCX_plot_final.R

DLPFC_plot_final.R

Code to generate biclustering plot

TCX_BranchPhenotype.R