scDataviz

DOI: 10.18129/B9.bioc.scDataviz    

This is the development version of scDataviz; for the stable release version, see scDataviz.

scDataviz: single cell dataviz and downstream analyses

Bioconductor version: Development (3.13)

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>

Citation (from within R, enter citation("scDataviz")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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, knitr, kableExtra
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_1.1.0.tar.gz
Windows Binary scDataviz_1.1.0.zip
macOS 10.13 (High Sierra) scDataviz_1.1.0.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

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