scTreeViz
R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations
Bioconductor version: Release (3.20)
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")):
Installation
To install this package, start R (version "4.4") 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 | 1.12.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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 | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scTreeViz_1.12.0.tar.gz |
| Windows Binary (x86_64) | scTreeViz_1.12.0.zip |
| macOS Binary (x86_64) | scTreeViz_1.12.0.tgz |
| macOS Binary (arm64) | scTreeViz_1.12.0.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 |