├── AdditionalAnalysis_External_ST_CRC_Dataset ├── 01_Clustering_Resolution_05.Rmd ├── 02_PathwayActivity.Rmd ├── 03_Tf_Activity.Rmd ├── 07_02_Misty_TFs_DE_Aggregated.Rmd ├── 07_Misty_TFs_DE_ligandsDE.Rmd ├── Pub_CMSCaller_PseudoBulkClassification.Rmd ├── Pub_Cell2LocPlots.Rmd ├── Pub_Pathway_CMS_correlation.Rmd ├── Pub_Proportion_Plots.Rmd ├── Pub_TF_CMS_correlation.Rmd └── README.md ├── CancerSEA_Scores ├── 14_InterPatient_Hetereogeneity_CancerSEA_profiles.Rmd └── README.md ├── CellCommunication ├── 14_InterPatient_Hetereogeneity_Dorothea_profiles.Rmd ├── 14_InterPatient_Hetereogeneity_Dorothea_profiles_PathoAnnotations.Rmd ├── 14_LigandReceptor_DorotheaClusters.Rmd ├── 14_LigandReceptor_DorotheaClusters_ExploringResults.Rmd ├── 22_Misty_TFsDE_ligandsDE.Rmd ├── 22_Misty_TFsDE_ligandsDE_AggregatedResults.Rmd ├── 23_graphGeneration_TopLigandReceptors.Rmd ├── 24_Liana_sc_CMS2.Rmd ├── 25_TFactivity_sc_CMS2.Rmd └── README.md ├── Deconvolution ├── ExternalST_SMC │ ├── 07b_Cell2Loc_Deconvolution-CRC_LiverMetastasis.ipynb │ └── README.md ├── InternalST_KUL3 │ ├── 07a_CEll2Loc_ExpressionSignature-KUL3_cohort.ipynb │ ├── 07b_Cell2Loc_Deconvolution-KUL3_cohort.ipynb │ ├── 07c_Cell2Loc_Deconvolution_Downstream_Analysis-KUL3_cohort.ipynb │ └── README.md ├── InternalST_SMC │ ├── 07a_CEll2Loc_ExpressionSignature.ipynb │ ├── 07b_Cell2Loc_Deconvolution.ipynb │ ├── 07c_Cell2Loc_Deconvolution_Downstream_Analysis.ipynb │ ├── Pub_Reading_Factors.R │ └── README.md └── README.md ├── Extras └── StudyOutline.png ├── FigureArrangement ├── Pub_XX_ArrangeCell2LocPlots.Rmd ├── Pub_XX_ArrangeCell2LocPlots_2.Rmd └── README.md ├── General_Analysis_perSample ├── 02_Clustering_Resolution_05.Rmd ├── 05_PathwayActivity.Rmd ├── 06_TF_Activity.Rmd └── README.md ├── General_Integrated_Analysis ├── Enrichment_DepletionPlots.Rmd ├── ProportionsCell2Loc_VS_Annotations.Rmd ├── Pub_03_Filtering_Normalization_JointClustering_CorrectSample.Rmd ├── Pub_XX_ClusteringReplicates_EvalDeconv_V2.Rmd ├── Pub_XX_correlation_pathway_CMS.Rmd ├── Pub_XX_correlation_tfs_CMS.Rmd └── README.md ├── InterPatient_Heterogeneity ├── 27_InterPatient_Het_UMAP_Harmony_OnlyCMS2.Rmd ├── 28_InterPatient_DEA_OnlyCMS2.Rmd ├── 29_InterPatient_PseudobulPathway_CMS2_TME.Rmd ├── 30_InterPatient_Pseudobulk_TFs_CMS2_TME.Rmd ├── ProportionsCMS2Tumor_OnlyTumor.Rmd └── README.md ├── IntraPatient_Heterogeneity ├── 32_02_IntraPatient_BayesSpace_SampleA121573_Rep1.Rmd ├── 32_03_IntraPatient_BayesSpace_SampleA121573_Rep1_PathwayActivity.Rmd ├── 34_GeneExpressionGradients_SampleA595688_Rep1.Rmd └── README.md ├── LICENSE ├── Quality_Control ├── 00_QC_GlobalMetrics.Rmd ├── 01_QC_ImageBased.Rmd └── README.md ├── README.md ├── Sample_Characterization ├── 37_Comparison_Korean_Belgian.Rmd ├── Pub_CMSCaller_PseudoBulkClassification.Rmd ├── Pub_CMScallerClassification_Pseudobulk.Rmd ├── Pub_Proportion_Plots.Rmd └── README.md └── WrapperFunction ├── 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