scBubbletree
Quantitative visual exploration of scRNA-seq data
Bioconductor version: Release (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("scBubbletree")):
Installation
To install this package, start R (version "4.4") 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")| User Manual: scBubbletree | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, RNASeq, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 |
| 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 | scBubbletree_1.6.0.tar.gz |
| Windows Binary (x86_64) | scBubbletree_1.6.0.zip |
| macOS Binary (x86_64) | scBubbletree_1.6.0.tgz |
| macOS Binary (arm64) | scBubbletree_1.6.0.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 |