Overview | Data | Dataset : Farmer et al 2017, Mouse lacrimal gland | Dataset : Watkins et al 2009, PBMC microarrays | Dataset : 10X genomics, pbmc4k, k=7 | Dataset : Zeisel et al 2015, Mouse brain | Dataset : Zheng et al 2017, Pure PBMCs | Use | References

Overview | Workflow | Prepare dataset | Within dataset differential expression | Query-Reference comparison | Output | Interpreting output | Assigning labels to clusters | Using the package | Installation | Quickstart | Prepare data | Input data | From tables or flat files | From 10X pipeline output | Directly with SummarizedExperiment objects | Handling large datasets | Reading microarray data | Input filtering and Pre-processing | Filtering cells and low-expression genes | Converting IDs | Within-experiment differential expression | Running comparisions | Compare groups to reference | Compare groups within a single dataset | Make labels for groups | Special case: Saving get_the_up_genes_for_all_possible_groups output | Example Analyses | PBMCs - 10X vs Microarray Reference | Prepare 10X query dataset | Prepare reference microarray dataset | Compare 10X query PBMCs to to reference | Mouse tissues - Similar and different | Load and compare mouse brain datasets | Load lacrimal gland dataset | Cross-tissue comparision | Session Info | References