DOI: 10.18129/B9.bioc.scTreeViz  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scTreeViz.

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

Bioconductor version: 3.16

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.

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

Maintainer: Jayaram Kancherla <jayaram.kancherla at>

Citation (from within R, enter citation("scTreeViz")):


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HTML R Script Explore Data using scTreeViz
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biocViews GUI, Infrastructure, SingleCell, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License Artistic-2.0
Depends R (>= 4.0), methods, epivizr, SummarizedExperiment
Imports data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils
Suggests knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb
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