scDataviz
scDataviz: single cell dataviz and downstream analyses
Bioconductor version: Release (3.20)
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("scDataviz")):
Installation
To install this package, start R (version "4.4") 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")| scDataviz: single cell dataviz and downstream analyses | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, FlowCytometry, GeneExpression, ImmunoOncology, MassSpectrometry, RNASeq, SingleCell, Software, Transcription |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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 |
| System Requirements | |
| URL | https://github.com/kevinblighe/scDataviz |
| Bug Reports | https://github.com/kevinblighe/scDataviz/issues |
See More
| Suggests | PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scDataviz_1.16.0.tar.gz |
| Windows Binary (x86_64) | scDataviz_1.16.0.zip |
| macOS Binary (x86_64) | scDataviz_1.16.0.tgz |
| macOS Binary (arm64) | scDataviz_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scDataviz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scDataviz |
| Bioc Package Browser | https://code.bioconductor.org/browse/scDataviz/ |
| Package Short Url | https://bioconductor.org/packages/scDataviz/ |
| Package Downloads Report | Download Stats |