scTreeViz
This is the released version of scTreeViz; for the devel version, see scTreeViz.
R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations
Bioconductor version: Release (3.23)
scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters.
Author: Jayaram Kancherla [aut, cre], Hector Corrada Bravo [aut], Kazi Tasnim Zinat [aut], Stephanie Hicks [aut]
Maintainer: Jayaram Kancherla <jayaram.kancherla at gmail.com>
citation("scTreeViz")):
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")
BiocManager::install("scTreeViz")
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("scTreeViz")| Explore Data using scTreeViz | HTML | R Script |
| Reference Manual |
Details
| biocViews | GUI, Infrastructure, SingleCell, Software, Visualization |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), methods, epivizr, SummarizedExperiment |
| Imports | data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb |
| 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 | scTreeViz_1.18.0.tar.gz |
| Windows Binary (x86_64) | scTreeViz_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | scTreeViz_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | scTreeViz_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scTreeViz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scTreeViz |
| Bioc Package Browser | https://code.bioconductor.org/browse/scTreeViz/ |
| Package Short Url | https://bioconductor.org/packages/scTreeViz/ |
| Package Downloads Report | Download Stats |