# R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

## Documentation for package ‘scTreeViz’ version 1.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

.generate_hierarchy_tree | generate hierarchy tree
.generate_leaf_of_table | generate leaf of table
.generate_nodes_table | generate nodes table tree
.generate_node_ids | generate node ids in the tree
.replaceNAFeatures | replace if there are NA's in the hierarchy
aggregateTree | show object
aggregateTree-method | show object
ClusterHierarchy | Creates a new ClusterHierarchy object.
ClusterHierarchy-class | ClusterHierarchy class to manage treeviz cluster data
createFromSCE | Creates a 'TreeViz" object from 'SingleCellExperiment'. Generates clusters based on Walktrap algorithm if no default is provided
createFromSeurat | Creates a 'TreeViz' object from 'Seurat'
createTreeViz | Creates 'TreeViz' object from hierarchy and count matrix
EpivizTreeData | Data container for MRexperiment objects
EpivizTreeData-class | Data container for MRexperiment objects
getNodes | Subset TreeIndex
getNodes-method | Subset TreeIndex
getNodeStates | Subset TreeIndex
getNodeStates-method | Subset TreeIndex
plot-method | show object
register-method | show object
set_gene_list | Sets gene list for visualization
show-method | Subset TreeIndex
show-method | show object
splitAt | Subset TreeIndex
splitAt-method | Subset TreeIndex
startTreeviz | Start treeviz app and create 'TreeVizApp' object to manage connection.
TreeIndex | create a new TreeIndex object
TreeIndex-class | TreeIndex class to manage and query hierarchical data
TreeViz | The TreeViz class.
TreeViz-class | TreeViz class wrapper for SummarizedExperiment objects
TreeVizApp | Class managing connection to metaviz application.
TreeVizApp-class | Class managing connection to metaviz application.
[-method | Subset TreeIndex