scTreeViz
R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scTreeViz")Details
| Maintainer | Jayaram Kancherla <jayaram.kancherla@gmail.com> |
| Author | Jayaram Kancherla [aut, cre], Hector Corrada Bravo [aut], Kazi Tasnim Zinat [aut], Stephanie Hicks [aut] |
| License | Artistic-2.0 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GUI, Infrastructure, SingleCell, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/scTreeViz/ |
Citation
From within R, enter citation("scTreeViz"):
Jayaram Kancherla, Hector Corrada Bravo, Kazi Tasnim Zinat, Stephanie Hicks. scTreeViz: R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations. doi:10.18129/B9.bioc.scTreeViz, R package version 1.18.0, https://bioconductor.org/packages/scTreeViz.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | scTreeViz_1.18.0.tgz |
| macOS binary (x86_64) | scTreeViz_1.18.0.tgz |
Dependencies
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
Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb