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scBubbletree

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

Quantitative visual exploration of scRNA-seq data


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

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

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

Details

biocViews Clustering, RNASeq, SingleCell, Software, Transcriptomics, Visualization
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements Python (>= 3.6), leidenalg (>= 0.8.2)
URL https://github.com/snaketron/scBubbletree
Bug Reports https://github.com/snaketron/scBubbletree/issues
See More
Suggests BiocStyle, knitr, testthat, cluster, SingleCellExperiment
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Build Report Build Report

Package Archives

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

Source Package scBubbletree_1.5.0.tar.gz
Windows Binary scBubbletree_1.5.0.zip
macOS Binary (x86_64) scBubbletree_1.5.0.tgz
macOS Binary (arm64) scBubbletree_1.5.0.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