dittoSeq
This is the development version of dittoSeq; for the stable release version, see dittoSeq.
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
Bioconductor version: Development (3.21)
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>
citation("dittoSeq")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| Annotating scRNA-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | ggplot2 |
| Imports | methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | SPIAT |
| Suggests Me | demuxSNP, tidySingleCellExperiment, magmaR, scCustomize |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dittoSeq_1.19.0.tar.gz |
| Windows Binary (x86_64) | dittoSeq_1.19.0.zip (64-bit only) |
| macOS Binary (x86_64) | dittoSeq_1.19.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/dittoSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dittoSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/dittoSeq/ |
| Package Short Url | https://bioconductor.org/packages/dittoSeq/ |
| Package Downloads Report | Download Stats |