Introduction | Load Package | Load Example Data | Quality control | Run BLISA at the LR level | Run BLISA at the pathway level | Visualization | Spatial Map of Hotspot Bins | Session Information

Introduction | Load Package | Load Example Data | Bin Cells into Hexagons | Run BLISA | Rank LR Pairs by Hotspot Count | Spatial Map of Hotspot Bins | Cell-Cell Interaction (CCI) Heatmaps | Across all LR pairs | For a single LR pair | Aggregated across LR pairs | Spatial Map of Dominant Cell-Type Pairs | Session Information

What is it? | How to get help | Further reading

Installation | Quick start | Load data | Grid-based analysis | Density calculation | Find Regions-of-interest (ROIs) | Detected by algorithm | Select ROI by user | Testing relationship between cell types | Cell-based analysis | cell annotation based on grid density

Abstract | Introduction | Description of the biological experiment | Preliminary analysis | Downloading the read counts | Adding gene annotation | Design matrix | Filtering to remove low counts | Library size normalization | Exploring differences between libraries | Dispersion estimation | Differential expression analysis | Testing for differential expression | Differential expression above a fold-change threshold | Heat map clustering | Analysis of deviance | Complicated contrasts | Pathway analysis | Gene ontology analysis | KEGG pathway analysis | FRY gene set tests | Camera gene set enrichment analysis | Packages used | Read alignment and quantification | Download raw sequence files from the SRA | Accuracy of base-calling | Build a genome index | Aligning reads | Quantifying read counts for each gene | Data and software availability | Author contributions | Grant information | Acknowledgments | How to cite | References