Package: scTreeViz 1.13.0

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]

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scTreeViz.pdf |scTreeViz.html✨
scTreeViz/json (API)

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

Peer review:

On BioConductor:scTreeViz-1.13.0(bioc 3.21)scTreeViz-1.12.0(bioc 3.20)

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 139 downloads 11 exports 246 dependencies

Last updated 2 months agofrom:9eebcab020. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winNOTEDec 19 2024
R-4.3-macNOTEDec 19 2024

Exports:aggregateTreeClusterHierarchycreateFromSCEcreateFromSeuratcreateTreeVizgetNodesshowsplitAtstartTreevizTreeIndexTreeViz

Dependencies:abindAnnotationDbiAnnotationFilteraskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularbiomaRtBiostringsbitbit64bitopsblobblusterbslibbumphuntercachemCairocaToolscheckmatecliclusterclustreecodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdoRNGdotCall64dplyrdqrngedgeRensembldbepivizrepivizrDataepivizrServerevaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggbeeswarmggforceggplot2ggraphggrastrggrepelggridgesglobalsgluegoftestgplotsgraphgraphlayoutsgridExtragtablegtoolsherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimeminiUImunsellnlmeopensslOrganismDbiparallellypatchworkpbapplypheatmappillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprogressprogressrpromisesProtGenericspurrrR6raggRANNrappdirsRBGLRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLRCurlreshape2restfulrreticulateRhtslibrjsonrlangrmarkdownrngtoolsROCRrprojrootRsamtoolsRSpectraRSQLitersvdrtracklayerRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermorescransctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingtibbletidygraphtidyrtidyselecttinytextweenrtxdbmakerUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioczoo

Interactively explore and visualize Single Cell RNA seq data

Jayaram Kancherla, Kazi Tasnim Zinat, Héctor Corrada Bravo

Rendered fromExploreTreeViz.Rmdusingknitr::rmarkdownon Dec 19 2024.

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