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FridleyLab/ccRCC_CosMx_SMI_2023

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9 Commits
0.1.Table1.R
0.1.Table1.R
 
 
1.KidneyCellAtlas_cleaning.R
1.KidneyCellAtlas_cleaning.R
 
 
10.1.abundance_io_associations_primaryTumor_manuscript-figure.R
10.1.abundance_io_associations_primaryTumor_manuscript-figure.R
 
 
10.3.abundance_sarcomatoid_associations.R
10.3.abundance_sarcomatoid_associations.R
 
 
10.6.2.uni_clustering_io_associations_primaryTumor_r150.R
10.6.2.uni_clustering_io_associations_primaryTumor_r150.R
 
 
10.8.2.uni_clustering_sarcomatoid_associations_r150.R
10.8.2.uni_clustering_sarcomatoid_associations_r150.R
 
 
11.0.1.2.bulk_diff_sarcomatoid.R
11.0.1.2.bulk_diff_sarcomatoid.R
 
 
11.0.1.bulk_diff_pre-postIO.R
11.0.1.bulk_diff_pre-postIO.R
 
 
11.0.2.tumor_stroma_gsea_cell-level_primaryIO.R
11.0.2.tumor_stroma_gsea_cell-level_primaryIO.R
 
 
11.1.2.STenrich_gsva-polygons.R
11.1.2.STenrich_gsva-polygons.R
 
 
11.1.2.STenrich_gsva.R
11.1.2.STenrich_gsva.R
 
 
11.4.2.tumor_stroma_gsea_cell-level_primaryIO_sarcomatoid.R
11.4.2.tumor_stroma_gsea_cell-level_primaryIO_sarcomatoid.R
 
 
11.4.tumor_stroma_gsea_cell-level_primaryIO.R
11.4.tumor_stroma_gsea_cell-level_primaryIO.R
 
 
11.5.CellTalkDB_LigandReceptor_BiMoransI_EMT.R
11.5.CellTalkDB_LigandReceptor_BiMoransI_EMT.R
 
 
11.5.CellTalkDB_LigandReceptor_BiMoransI_IL6.R
11.5.CellTalkDB_LigandReceptor_BiMoransI_IL6.R
 
 
11.6.mIF_marker_identification.R
11.6.mIF_marker_identification.R
 
 
12.1.validation_mIF_creation-uniK.R
12.1.validation_mIF_creation-uniK.R
 
 
12.2.validation_mIF_creation-biK.R
12.2.validation_mIF_creation-biK.R
 
 
12.3.SavingValidationDerived.R
12.3.SavingValidationDerived.R
 
 
12.4.5.ligand-receptor_abundance_tophenotype.R
12.4.5.ligand-receptor_abundance_tophenotype.R
 
 
12.4.ligand-receptor_abundance-betabinomial.R
12.4.ligand-receptor_abundance-betabinomial.R
 
 
12.5.ligand-receptor_bivarK.R
12.5.ligand-receptor_bivarK.R
 
 
2.1.Cell_count_by_fov_primary.R
2.1.Cell_count_by_fov_primary.R
 
 
2.ExploreSMI_Manley.Rmd
2.ExploreSMI_Manley.Rmd
 
 
3.FineTuningAnnotations.Rmd
3.FineTuningAnnotations.Rmd
 
 
3D_PCA.R
3D_PCA.R
 
 
4.KCA_expression_profile.R
4.KCA_expression_profile.R
 
 
5.CellTyping.Rmd
5.CellTyping.Rmd
 
 
6.5.Exploring_Tcell_InsutypeSubCluster1.R
6.5.Exploring_Tcell_InsutypeSubCluster1.R
 
 
6.6.modeling_tumor-v-normal_fixedFOV.R
6.6.modeling_tumor-v-normal_fixedFOV.R
 
 
6.7.final_cell_types.Rmd
6.7.final_cell_types.Rmd
 
 
6.8.Polygon_plots_with_curated_tumor.R
6.8.Polygon_plots_with_curated_tumor.R
 
 
6.FineTuningInsitutype.Rmd
6.FineTuningInsitutype.Rmd
 
 
7.1.making_mif_papillary.R
7.1.making_mif_papillary.R
 
 
7.making_mif.R
7.making_mif.R
 
 
8.1.computing_univariatek.R
8.1.computing_univariatek.R
 
 
8.1.computing_univariatek_papillary.R
8.1.computing_univariatek_papillary.R
 
 
8.2.computing_bivariatek_papillary.R
8.2.computing_bivariatek_papillary.R
 
 
8.3.computing_bivariateG_papillary.R
8.3.computing_bivariateG_papillary.R
 
 
9.1.visualize_univariateK.R
9.1.visualize_univariateK.R
 
 
9.1.visualize_univariateK_papillary.R
9.1.visualize_univariateK_papillary.R
 
 
9.2.visualize_bivariateK_papillary.R
9.2.visualize_bivariateK_papillary.R
 
 
9.2.visualize_bivariateK_papillary_1000perms.R
9.2.visualize_bivariateK_papillary_1000perms.R
 
 
README.md
README.md
 
 

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