scBubbletree

DOI: 10.18129/B9.bioc.scBubbletree    

Quantitative visual exploration of scRNA-seq data

Bioconductor version: Release (3.16)

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>

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

Installation

To install this package, start R (version "4.2") 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 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3 + file LICENSE
Depends R (>= 4.2.0)
Imports reshape2, future, future.apply, ape, scales, Seurat, ggplot2, ggtree, patchwork, 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_1.0.0.tar.gz
Windows Binary scBubbletree_1.0.0.zip
macOS Binary (x86_64) scBubbletree_1.0.0.tgz
macOS Binary (arm64) scBubbletree_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scBubbletree
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scBubbletree
Package Short Url https://bioconductor.org/packages/scBubbletree/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: