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

Bioconductor version: Release (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Explore Data using scTreeViz HTML R Script
Reference Manual PDF


biocViews GUI, Infrastructure, SingleCell, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
System Requirements
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Suggests knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb
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Follow Installation instructions to use this package in your R session.

Source Package scTreeViz_1.10.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) scTreeViz_1.10.0.tgz
macOS Binary (arm64) scTreeViz_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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