ST_LUAD

Spatial Transcriptomics Delineate Dedifferentiation and Molecular Characterizations in Lung Adenocarcinoma Progression

Features

Seurat (V3.2)
Monocle (V2.18.0)
CytoTRACE (V0.3.3)
clusterProfiler (V3.16.1)
SCENIC (V 1.2.2)
GSVA (V1.32.0)
MSigDB (V7.3)
Cytoscape (V3.6.0)
CellPhoneDB (V2.1.4)
inForm (V2.4)
QuPath (V0.2.0)
survival (V3.2-10)
survminer (V0.4.6)
R package: stats (V3.6.0), FSA (V0.9.1), e1071 (V1.7-3), pheatmap (V1.0.12), psych (V1.9.12.31)

Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
Fig1_DimensionalityReduction_clustering_FindMarkers.R		Fig1_DimensionalityReduction_clustering_FindMarkers.R
Fig1_demo.Rdata.txt		Fig1_demo.Rdata.txt
Fig2A_CellType_percent		Fig2A_CellType_percent
Fig2A_annotation.R		Fig2A_annotation.R
Fig2A_heatmap_for_plot_demo.txt		Fig2A_heatmap_for_plot_demo.txt
Fig2A_plot.R		Fig2A_plot.R
Fig2B_Hamming_Distance.R		Fig2B_Hamming_Distance.R
Fig2B_input_demo.txt		Fig2B_input_demo.txt
Fig2C_D_cellular_type.R		Fig2C_D_cellular_type.R
Fig2C_D_subtype_for_plot_demo.txt		Fig2C_D_subtype_for_plot_demo.txt
Fig2E_MIA.R		Fig2E_MIA.R
Fig2E_hearmap.R		Fig2E_hearmap.R
Fig2E_heatmap_TAM_forplot_demo.txt		Fig2E_heatmap_TAM_forplot_demo.txt
Fig3A_B_CytoTRACE_for_plot.pl		Fig3A_B_CytoTRACE_for_plot.pl
Fig3A_B_F_differentiation.R		Fig3A_B_F_differentiation.R
Fig3A_B_subtype_cluster_demo.txt		Fig3A_B_subtype_cluster_demo.txt
Fig3D_density.R		Fig3D_density.R
Fig4_Regulon.R		Fig4_Regulon.R
Fig5A_GSEA.R		Fig5A_GSEA.R
Fig5A_GSVA_subtype_every_spot.pl		Fig5A_GSVA_subtype_every_spot.pl
Fig5C_Jaccard_index.R		Fig5C_Jaccard_index.R
Fig6F_ligand_receptor_pairs.sh		Fig6F_ligand_receptor_pairs.sh
Fig7B_co-localization.R		Fig7B_co-localization.R
Fig7B_mIHC_subtype_density_all_positive_selected_format.txt		Fig7B_mIHC_subtype_density_all_positive_selected_format.txt
Fig7D_mIHC_cell_positive_distance2.pl		Fig7D_mIHC_cell_positive_distance2.pl
FigS4_ST_P5.transfer		FigS4_ST_P5.transfer
FigS4_co-occurrence.R		FigS4_co-occurrence.R
LICENSE		LICENSE
README.md		README.md