scBubbletree

DOI: 10.18129/B9.bioc.scBubbletree  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scBubbletree.

Quantitative visual exploration of scRNA-seq data

Bioconductor version: 3.17

scBubbletree is a quantitative method for visual exploration of scRNA-seq data. It preserves biologically meaningful properties of scRNA-seq data, such as local and global cell distances, as well as the density distribution of cells across the sample. scBubbletree is scalable and avoids the overplotting problem, and is able to visualize diverse cell attributes derived from multiomic single-cell experiments. Importantly, Importantly, scBubbletree is easy to use and to integrate with popular approaches for scRNA-seq data analysis.

Author: Simo Kitanovski [aut, cre]

Maintainer: Simo Kitanovski <simokitanovski at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("scBubbletree")

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("scBubbletree")

 

HTML	R Script	User Manual: scBubbletree
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, RNASeq, SingleCell, Software, Transcriptomics, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2.0)
Imports	reshape2, future, future.apply, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils
LinkingTo
Suggests	BiocStyle, knitr, testthat, cluster, SingleCellExperiment
SystemRequirements	Python (>= 3.6), leidenalg (>= 0.8.2)
Enhances
URL	https://github.com/snaketron/scBubbletree
BugReports	https://github.com/snaketron/scBubbletree/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scBubbletree_1.2.0.tar.gz
Windows Binary	scBubbletree_1.2.0.zip
macOS Binary (x86_64)	scBubbletree_1.2.0.tgz
macOS Binary (arm64)	scBubbletree_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scBubbletree
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scBubbletree
Bioc Package Browser	https://code.bioconductor.org/browse/scBubbletree/
Package Short Url	https://bioconductor.org/packages/scBubbletree/
Package Downloads Report	Download Stats