scTreeViz

DOI: 10.18129/B9.bioc.scTreeViz    

R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

Bioconductor version: Release (3.14)

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 (from within R, enter citation("scTreeViz")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML R Script Explore Data using scTreeViz
PDF   Reference Manual

Details

biocViews GUI, Infrastructure, SingleCell, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
LinkingTo
Suggests knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scTreeViz_1.0.0.tar.gz
Windows Binary scTreeViz_1.0.0.zip
macOS 10.13 (High Sierra) scTreeViz_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scTreeViz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scTreeViz
Package Short Url https://bioconductor.org/packages/scTreeViz/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: