Introduction | Package Installation and other requirements | Spatial Transcriptomics Data | Reference-free Deconvolution | Cell-type Annotation via annotated single-cell reference | Cell-type Annotation via known marker genes | Results and visualization | Figure 4A: Proportion of different cell types in the tissue. | Figure 4C: Localization of cell types with the dominant cell type in each spot | Figure 4D: Gene expression of Epithelial marker genes across spots | Figure 4E: Proportion of Epithelial cells across spots | Figure 5A: Proportion of different cell types in different spots | Figure 5D: Spots with 1 dominant cell type i.e., proportion > 0.5 | Figure 5E: Co-localized spots for Epithelial cells | Figure 6C: Concordance between expression profiles of found genes obtained from RETROFIT and scRNA-seq data | Session information

Introduction | Package Installation | Spatial Transcriptomics Data | Deconvolution | Cell-type Annotation | Deconvolution and annotation in one step (Optional) | Results | Session information