Registration and Call for Abstracts Open for Bioc2024

scTreeViz

This is the development version of scTreeViz; for the stable release version, see scTreeViz.

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


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scTreeViz")

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

Documentation

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

browseVignettes("scTreeViz")
Explore Data using scTreeViz HTML R Script
Reference Manual PDF

Details

biocViews GUI, Infrastructure, SingleCell, Software, Visualization
Version 1.9.0
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
URL
See More
Suggests knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scTreeViz_1.9.0.tar.gz
Windows Binary scTreeViz_1.9.0.zip (64-bit only)
macOS Binary (x86_64) scTreeViz_1.9.0.tgz
macOS Binary (arm64) scTreeViz_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scTreeViz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scTreeViz
Bioc Package Browser https://code.bioconductor.org/browse/scTreeViz/
Package Short Url https://bioconductor.org/packages/scTreeViz/
Package Downloads Report Download Stats