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Name		Name	Last commit message	Last commit date
CD14/cleaning		CD14/cleaning
CD14_Monocytes/cleaning		CD14_Monocytes/cleaning
FDR_analisysResults_files/execute-results		FDR_analisysResults_files/execute-results
Results		Results
Temp		Temp
__pycache__		__pycache__
_freeze		_freeze
celltypist_annotation_files/libs		celltypist_annotation_files/libs
docs		docs
e15.0_FD_CheckClustersUniformity		e15.0_FD_CheckClustersUniformity
src		src
.gitignore		.gitignore
.nojekyll		.nojekyll
AntibodyClusters.xlsx		AntibodyClusters.xlsx
BarPlot.afdesign		BarPlot.afdesign
CD14Figure.afdesign		CD14Figure.afdesign
CD14_background_ORA.txt		CD14_background_ORA.txt
CD14_cl-1_ORA.txt		CD14_cl-1_ORA.txt
CD14_cl1_ORA.txt		CD14_cl1_ORA.txt
CD14_cl2_ORA.txt		CD14_cl2_ORA.txt
CD14_cl3_ORA.txt		CD14_cl3_ORA.txt
CD14_cl4_ORA.txt		CD14_cl4_ORA.txt
CD14_cl5_ORA.txt		CD14_cl5_ORA.txt
Calinski_Harabasz.pdf		Calinski_Harabasz.pdf
Calinski_HarabaszFromProb.pdf		Calinski_HarabaszFromProb.pdf
ClusterSplitting.R		ClusterSplitting.R
Cluster_-1.txt		Cluster_-1.txt
Cluster_1.txt		Cluster_1.txt
Cluster_2.txt		Cluster_2.txt
Cluster_3.txt		Cluster_3.txt
Cluster_4.txt		Cluster_4.txt
Cluster_5.txt		Cluster_5.txt
ClusteringToolsComparison.pdf		ClusteringToolsComparison.pdf
ClusteringToolsComparison.png		ClusteringToolsComparison.png
ClusteringToolsDaviesBouldin.png		ClusteringToolsDaviesBouldin.png
ClusteringToolsSilhouette.png		ClusteringToolsSilhouette.png
ClusterizationsGDI_AllForebrainDorsal.log		ClusterizationsGDI_AllForebrainDorsal.log
CoexAssess.R		CoexAssess.R
CollectDataForGDITh.R		CollectDataForGDITh.R
CorticalCells_GSM2861511_E135-analysis.log		CorticalCells_GSM2861511_E135-analysis.log
CorticalCells_GSM2861511_E135-analysis.qmd		CorticalCells_GSM2861511_E135-analysis.qmd
CorticalCells_GSM2861511_E135_Scampy_expression_all_genes.gz		CorticalCells_GSM2861511_E135_Scampy_expression_all_genes.gz
CorticalCells_GSM2861514_E175-analysis.qmd		CorticalCells_GSM2861514_E175-analysis.qmd
CorticalCells_GSM2861514_E175_Scampy_expression_all_genes.gz		CorticalCells_GSM2861514_E175_Scampy_expression_all_genes.gz
DEA_Seurat_COTAN.qmd		DEA_Seurat_COTAN.qmd
DEA_Type1Er.qmd		DEA_Type1Er.qmd
Davies_Bouldin.pdf		Davies_Bouldin.pdf
Davies_BouldinFromProb.pdf		Davies_BouldinFromProb.pdf
DecisionTree_Analysis.R		DecisionTree_Analysis.R
FDR_DataSetCreation_ByClusterMerging.qmd		FDR_DataSetCreation_ByClusterMerging.qmd
FDR_analisys.qmd		FDR_analisys.qmd
FDR_analisysResults.rmarkdown		FDR_analisysResults.rmarkdown
FDR_analisysResults3_10.qmd		FDR_analisysResults3_10.qmd
FDR_analisysResults3_10_th04.qmd		FDR_analisysResults3_10_th04.qmd
FDR_analisysResults5.qmd		FDR_analisysResults5.qmd
FDR_analisysResults5_20.qmd		FDR_analisysResults5_20.qmd
FDR_analysisResultsLFC.qmd		FDR_analysisResultsLFC.qmd
FindUniformOrigCluster.qmd		FindUniformOrigCluster.qmd
ForebrainDorsal_E135-analysis.qmd		ForebrainDorsal_E135-analysis.qmd
ForebrainDorsal_E150-analysis.log		ForebrainDorsal_E150-analysis.log
ForebrainDorsal_E150-analysis.qmd		ForebrainDorsal_E150-analysis.qmd
ForebrainDorsal_E175-analysis.log		ForebrainDorsal_E175-analysis.log
ForebrainDorsal_E175-analysis.qmd		ForebrainDorsal_E175-analysis.qmd
ForebrainDorsal_MixingUniformClusters_ToEstimateGDISensitivity.qmd		ForebrainDorsal_MixingUniformClusters_ToEstimateGDISensitivity.qmd
ForebrainLaManno2021ClustersGDI.qmd		ForebrainLaManno2021ClustersGDI.qmd
GDI_Increment_From_Mixing.qmd		GDI_Increment_From_Mixing.qmd
GDI_Th_analysis.R		GDI_Th_analysis.R
GDI_vairance.qmd		GDI_vairance.qmd
LR_forUTClusters.qmd		LR_forUTClusters.qmd
MixingClustersGDI_ForebrainDorsal.log		MixingClustersGDI_ForebrainDorsal.log
MouseCortex_E14.5_Scampy_expression_all_genes.gz		MouseCortex_E14.5_Scampy_expression_all_genes.gz
MouseCortex_E14.5_analysis.Rmd		MouseCortex_E14.5_analysis.Rmd
MouseCortex_E14.5_analysis.log		MouseCortex_E14.5_analysis.log
Mouse_Cortex_E14.5.qmd		Mouse_Cortex_E14.5.qmd
NonCT_clusters.qmd		NonCT_clusters.qmd
OriginalClustersDistanceEvaluation.Rmd		OriginalClustersDistanceEvaluation.Rmd
OriginalClustersDistanceEvaluation.qmd		OriginalClustersDistanceEvaluation.qmd
PBMC1_filtering.qmd		PBMC1_filtering.qmd
PBMC2_filtering.qmd		PBMC2_filtering.qmd
PBMC3_filtering.qmd		PBMC3_filtering.qmd
PBMC4_filtering.qmd		PBMC4_filtering.qmd
PBMC_clusteringNew2025.qmd		PBMC_clusteringNew2025.qmd
Project_Cluster_1.zip		Project_Cluster_1.zip
Project_Cluster_2.zip		Project_Cluster_2.zip
Project_Cluster_3.zip		Project_Cluster_3.zip
Project_Cluster_5.zip		Project_Cluster_5.zip
Project_Cluster__1.zip		Project_Cluster__1.zip
Real_UT_clustersByCotan.qmd		Real_UT_clustersByCotan.qmd
Report_Cluster_1.html		Report_Cluster_1.html
Report_Cluster_2.html		Report_Cluster_2.html
Report_Cluster_3.html		Report_Cluster_3.html
Report_Cluster_5.html		Report_Cluster_5.html
Report_Cluster__1.html		Report_Cluster__1.html
Silhouette.pdf		Silhouette.pdf
SilhouetteFromProb.pdf		SilhouetteFromProb.pdf
SomeNumerosity.txt		SomeNumerosity.txt
SubsettingDataSensitivityEvaluation.qmd		SubsettingDataSensitivityEvaluation.qmd
SuppTable1.xlsx		SuppTable1.xlsx
_quarto.yml		_quarto.yml
aam8999_tables6.xlsx		aam8999_tables6.xlsx
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