Package: scTreeViz 1.19.0

Jayaram Kancherla

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

scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters.

Authors:Jayaram Kancherla [aut, cre], Hector Corrada Bravo [aut], Kazi Tasnim Zinat [aut], Stephanie Hicks [aut]

scTreeViz_1.19.0.tar.gz
scTreeViz_1.19.0.zip(r-4.7)scTreeViz_1.19.0.zip(r-4.6)scTreeViz_1.19.0.zip(r-4.5)
scTreeViz_1.19.0.tgz(r-4.6-any)scTreeViz_1.19.0.tgz(r-4.5-any)
scTreeViz_1.19.0.tar.gz(r-4.7-any)scTreeViz_1.19.0.tar.gz(r-4.6-any)
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manual.pdf |manual.html✨
card.svg |card.png
scTreeViz/json (API)

# Install 'scTreeViz' in R:
install.packages('scTreeViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:scTreeViz-1.19.0(bioc 3.24)scTreeViz-1.18.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualizationinfrastructureguisinglecell

4.00 score 3 scripts 342 downloads 11 exports 233 dependencies

Last updated from:dd15f61111. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

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bioc-checksNOTE353
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source / vignettesOK535
linux-release-x86_64WARNING683
macos-release-arm64WARNING436
macos-oldrel-arm64WARNING331
windows-develWARNING1888
windows-releaseWARNING1448
windows-oldrelWARNING1719
wasm-releaseOK273

Exports:aggregateTreeClusterHierarchycreateFromSCEcreateFromSeuratcreateTreeVizgetNodesshowsplitAtstartTreevizTreeIndexTreeViz

Dependencies:abindAnnotationDbiAnnotationFilteraskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64bitopsblobblusterbslibbumphuntercachemCairocaToolscheckmatecigarillocliclusterclustreecodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydeldirdigestdoRNGdotCall64dplyrdqrngedgeRensembldbepivizrepivizrDataepivizrServerevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbeeswarmggforceggplot2ggraphggrastrggrepelggridgesglobalsgluegoftestgplotsgraphgraphlayoutsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmimeminiUInlmeopensslOrganismDbiotelparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisesProtGenericspurrrR6raggRANNrappdirsRBGLRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLRCurlreshape2restfulrreticulateRhtslibrjsonrlangrmarkdownrngtoolsROCRrprojrootRsamtoolsRSpectraRSQLitersvdrtracklayerRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscattermorescransctransformscuttleSeqinfoSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidygraphtidyrtidyselecttinytextweenrUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXMLxtableXVectoryamlzoo

Interactively explore and visualize Single Cell RNA seq data

Jayaram Kancherla, Kazi Tasnim Zinat, Héctor Corrada Bravo

Rendered fromExploreTreeViz.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-08-21
Started: 2020-07-08

Readme and manuals

Help Manual

Help pageTopics
generate hierarchy tree.generate_hierarchy_tree
generate leaf of table.generate_leaf_of_table
generate node ids in the tree.generate_node_ids
generate nodes table tree.generate_nodes_table
replace if there are NA's in the hierarchy.replaceNAFeatures
Subset TreeIndexgetNodes getNodes,TreeIndex-method getNodeStates getNodeStates,TreeIndex-method show,TreeIndex-method splitAt splitAt,TreeIndex-method [,TreeIndex,ANY,ANY,ANY-method
Creates a new ClusterHierarchy object.ClusterHierarchy
ClusterHierarchy class to manage treeviz cluster dataClusterHierarchy-class
Creates a `TreeViz`` object from `SingleCellExperiment`. Generates clusters based on Walktrap algorithm if no default is providedcreateFromSCE
Creates a `TreeViz` object from `Seurat`createFromSeurat
Creates `TreeViz` object from hierarchy and count matrixcreateTreeViz
Data container for MRexperiment objectsEpivizTreeData EpivizTreeData-class
Sets gene list for visualizationset_gene_list
show objectaggregateTree aggregateTree,TreeViz-method plot,TreeViz,ANY-method register,TreeViz-method show,TreeViz-method
Start treeviz app and create 'TreeVizApp' object to manage connection.startTreeviz
create a new TreeIndex objectTreeIndex
TreeIndex class to manage and query hierarchical dataTreeIndex-class
The TreeViz class.TreeViz
TreeViz class wrapper for SummarizedExperiment objectsTreeViz-class
Class managing connection to metaviz application.TreeVizApp TreeVizApp-class