Package: scTreeViz 1.11.0

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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# Install 'scTreeViz' in R:

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

On BioConductor:scTreeViz-1.11.0(bioc 3.20)scTreeViz-1.10.0(bioc 3.19)

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

bioconductor-package

11 exports 0.82 score 246 dependencies

Last updated 2 months agofrom:ce68a1dab7

Exports:aggregateTree ClusterHierarchy createFromSCE createFromSeurat createTreeViz getNodes show splitAt startTreeviz TreeIndex TreeViz

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc beachmat beeswarm BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocNeighbors BiocParallel BiocSingular biomaRt Biostrings bit bit64 bitops blob bluster bslib bumphunter cachem Cairo caTools checkmate cli cluster clustree codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir digest doRNG dotCall64 dplyr dqrng edgeR ensembldb epivizr epivizrData epivizrServer evaluate fansi farver fastDummies fastmap filelock fitdistrplus FNN fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggbeeswarm ggforce ggplot2 ggraph ggrastr ggrepel ggridges globals glue goftest gplots graph graphlayouts gridExtra gtable gtools here highr hms htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leiden lifecycle limma listenv lmtest locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mgcv mime miniUI munsell nlme openssl OrganismDbi parallelly patchwork pbapply pheatmap pillar pkgconfig plogr plotly plyr png polyclip prettyunits progress progressr promises ProtGenerics purrr R6 ragg RANN rappdirs RBGL RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress RcppTOML RCurl reshape2 restfulr reticulate Rhtslib rjson rlang rmarkdown rngtools ROCR rprojroot Rsamtools RSpectra RSQLite rsvd rtracklayer Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scater scattermore scran sctransform scuttle Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.utils statmod stringi stringr SummarizedExperiment survival sys systemfonts tensor textshaping tibble tidygraph tidyr tidyselect tinytex tweenr txdbmaker UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr xfun XML xml2 xtable XVector yaml zlibbioc zoo

Interactively explore and visualize Single Cell RNA seq data

Jayaram Kancherla, Kazi Tasnim Zinat, Héctor Corrada Bravo

Rendered fromExploreTreeViz.Rmdusingknitr::rmarkdownon Jun 30 2024.

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

Help page	Topics
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 TreeIndex	getNodes 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 data	ClusterHierarchy-class
Creates a `TreeViz`` object from `SingleCellExperiment`. Generates clusters based on Walktrap algorithm if no default is provided	createFromSCE
Creates a `TreeViz` object from `Seurat`	createFromSeurat
Creates `TreeViz` object from hierarchy and count matrix	createTreeViz
Data container for MRexperiment objects	EpivizTreeData EpivizTreeData-class
Sets gene list for visualization	set_gene_list
show object	aggregateTree 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 object	TreeIndex
TreeIndex class to manage and query hierarchical data	TreeIndex-class
The TreeViz class.	TreeViz
TreeViz class wrapper for SummarizedExperiment objects	TreeViz-class
Class managing connection to metaviz application.	TreeVizApp TreeVizApp-class

Package: scTreeViz 1.11.0

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

Interactively explore and visualize Single Cell RNA seq data

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