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("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 | ||
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 |