scDotPlot
Cluster a Single-cell RNA-seq Dot Plot
Bioconductor version: Release (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")
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 | 1.0.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | scDotPlot_1.0.0.zip |
| macOS Binary (x86_64) | scDotPlot_1.0.0.tgz |
| macOS Binary (arm64) | scDotPlot_1.0.0.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 |