A Shiny App Demonstrating a Query-Reference Mapping Algorithm
for Single-Cell Data
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Documentation for package ‘Azimuth’ version 0.5.0
Help Pages
| Azimuth-package | Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data |
| Azimuth | Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data |
| AzimuthApp | Launch the mapping app |
| AzimuthBridgeReference | Create a Seurat object compatible with Azimuth. |
| AzimuthData | AzimuthData |
| AzimuthData-class | AzimuthData |
| AzimuthReference | Create a Seurat object compatible with Azimuth. |
| ConvertGeneNames | Converts gene names of query to match type/species of reference names (human or mouse). |
| CreateAzimuthData | Create an 'AzimuthData' object |
| CreateColorMap | Create A Color Map |
| GetColorMap | Get Azimuth color mapping |
| GetColorMap.AzimuthData | Get Azimuth color mapping |
| GetColorMap.Seurat | Get Azimuth color mapping |
| GetPlotRef | Get Azimuth plotref |
| GetPlotRef.AzimuthData | Get Azimuth plotref |
| GetPlotRef.Seurat | Get Azimuth plotref |
| GetTranscripts | Get transcripts modified from Signac::GeneActivity |
| LoadBridgeReference | Load the extended reference RDS file for bridge integration |
| LoadFileInput | Load file input into a 'Seurat' object |
| LoadH5ADobs | Load obs from a H5AD file |
| LoadReference | Load the reference RDS files |
| ReferenceVersion | Get Azimuth reference version number |
| ReferenceVersion.AzimuthData | Get Azimuth reference version number |
| ReferenceVersion.Seurat | Get Azimuth reference version number |
| RunAzimuth | Run Azimuth annotation |
| RunAzimuth.character | Run Azimuth annotation |
| RunAzimuth.Seurat | Run Azimuth annotation |
| RunAzimuthATAC | Run Azimuth annotation for ATAC query |
| RunAzimuthATAC.character | Run Azimuth annotation for ATAC query |
| RunAzimuthATAC.Seurat | Run Azimuth annotation for ATAC query |
| SaveAzimuthReference | Save 'Azimuth' references and neighbors index to same folder |
| SetColorMap | Set Azimuth color mapping |
| SetColorMap.AzimuthData | Set Azimuth color mapping |
| SetColorMap.Seurat | Set Azimuth color mapping |
| ValidateAzimuthReference | Validate References for Azimuth |