Spatial Transcriptomics Delineate Dedifferentiation and Molecular Characterizations in Lung Adenocarcinoma Progression
- Dimensionality Reduction, clustering, FindMarkers
- Cell type mapping and deconvolution
- Spatial correlation analysis
- Multimodal intersection analysis (MIA)
- Dedifferentiation trajectory inference
- Gene Ontology Enrichment Analysis
- Jaccard index
- Spatial ligand-receptor interaction analysis
- mIHC image quantifications
- 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)
- Linux x86_64 GNU/Linux or UNIX
- R >= 3.6.0
- perl >= v5.16.3