scDataviz

DOI: 10.18129/B9.bioc.scDataviz    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see scDataviz.

scDataviz: single cell dataviz and downstream analyses

Bioconductor version: 3.15

In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease.

Author: Kevin Blighe [aut, cre]

Maintainer: Kevin Blighe <kevin at clinicalbioinformatics.co.uk>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scDataviz")

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("scDataviz")

 

HTML	R Script	scDataviz: single cell dataviz and downstream analyses
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, FlowCytometry, GeneExpression, ImmunoOncology, MassSpectrometry, RNASeq, SingleCell, Software, Transcription
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	GPL-3
Depends	R (>= 4.0), S4Vectors, SingleCellExperiment
Imports	ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods
LinkingTo
Suggests	PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/kevinblighe/scDataviz
BugReports	https://github.com/kevinblighe/scDataviz/issues
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	scDataviz_1.6.0.tar.gz
Windows Binary	scDataviz_1.6.0.zip
macOS Binary (x86_64)	scDataviz_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scDataviz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scDataviz
Package Short Url	https://bioconductor.org/packages/scDataviz/
Package Downloads Report	Download Stats