scTreeViz

DOI: 10.18129/B9.bioc.scTreeViz    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	Explore Data using scTreeViz
PDF		Reference Manual

Details

biocViews	GUI, Infrastructure, SingleCell, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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
LinkingTo
Suggests	knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	scTreeViz_1.2.0.tar.gz
Windows Binary	scTreeViz_1.2.0.zip
macOS Binary (x86_64)	scTreeViz_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scTreeViz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scTreeViz
Package Short Url	https://bioconductor.org/packages/scTreeViz/
Package Downloads Report	Download Stats