dittoSeq

DOI: 10.18129/B9.bioc.dittoSeq    

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

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

Bioconductor version: 3.15

A universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. Visualizations include dimensionality reduction plots, heatmaps, scatterplots, percent composition or expression across groups, and more. Customizations range from size and title adjustments to automatic generation of annotations for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton plot, hidden data overlay upon cursor hovering via ggplotly conversion, and many more. All with simple, discrete inputs. Color blindness friendliness is powered by legend adjustments (enlarged keys), and by allowing the use of shapes or letter-overlay in addition to the carefully selected dittoColors().

Author: Daniel Bunis [aut, cre], Jared Andrews [aut, ctb]

Maintainer: Daniel Bunis <daniel.bunis at ucsf.edu>

Installation

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

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

BiocManager::install("dittoSeq")

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("dittoSeq")

 

HTML	R Script	Annotating scRNA-seq data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics, Visualization
Version	1.8.1
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	MIT + file LICENSE
Depends	ggplot2
Imports	methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors
LinkingTo
Suggests	plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	escape, tidySingleCellExperiment
Links To Me
Build Report

Package Archives

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

Source Package	dittoSeq_1.8.1.tar.gz
Windows Binary	dittoSeq_1.8.1.zip (64-bit only)
macOS Binary (x86_64)	dittoSeq_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/dittoSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dittoSeq
Package Short Url	https://bioconductor.org/packages/dittoSeq/
Package Downloads Report	Download Stats