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 (3.24)
scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation.
Author: Simo Kitanovski [aut, cre]
Maintainer: Simo Kitanovski <simokitanovski at gmail.com>
citation("scBubbletree")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, RNASeq, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.2.0) |
| Imports | reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr |
| 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | scBubbletree_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | scBubbletree_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | scBubbletree_1.15.0.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 |