scDotPlot

This is the development version of scDotPlot; to use it, please install the devel version of Bioconductor.

Cluster a Single-cell RNA-seq Dot Plot


Bioconductor version: Development (3.20)

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

Author: Benjamin I Laufer [aut, cre], Brad A Friedman [aut]

Maintainer: Benjamin I Laufer <blaufer at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("scDotPlot")

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("scDotPlot")
scDotPlot HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcription, Visualization
Version 0.99.4
In Bioconductor since BioC 3.20 (R-4.4)
License Artistic-2.0
Depends R (>= 4.4.0)
Imports aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree, grDevices, magrittr, purrr, rlang, scales, scater, Seurat, SingleCellExperiment, stats, stringr, tibble, tidyr
System Requirements
URL https://github.com/ben-laufer/scDotPlot
Bug Reports https://github.com/ben-laufer/scDotPlot/issues
See More
Suggests AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr
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 scDotPlot_0.99.4.tar.gz
Windows Binary scDotPlot_0.99.4.zip
macOS Binary (x86_64) scDotPlot_0.99.4.tgz
macOS Binary (arm64) scDotPlot_0.99.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/scDotPlot
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scDotPlot
Bioc Package Browser https://code.bioconductor.org/browse/scDotPlot/
Package Short Url https://bioconductor.org/packages/scDotPlot/
Package Downloads Report Download Stats