schex

DOI: 10.18129/B9.bioc.schex    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see schex.

Hexbin plots for single cell omics data

Bioconductor version: 3.11

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment and SeuratObject. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.

Author: Saskia Freytag

Maintainer: Saskia Freytag <saskia.freytag at perkins.uwa.edu.au>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("schex")

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("schex")

 

HTML	R Script	multi_modal_schex
HTML	R Script	picking_the_right_resolution
HTML	R Script	Seurat_schex
HTML	R Script	shiny_schhex
HTML	R Script	using_schex
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, Sequencing, SingleCell, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	GPL-3
Depends	SingleCellExperiment(>= 1.7.4), Seurat, ggplot2 (>= 3.2.1), shiny
Imports	hexbin, stats, methods, cluster, dplyr, entropy, ggforce, scales, grid, concaveman
LinkingTo
Suggests	ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran
SystemRequirements
Enhances
URL	https://github.com/SaskiaFreytag/schex
BugReports	https://github.com/SaskiaFreytag/schex/issues
Depends On Me
Imports Me	scTensor, scTGIF
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	schex_1.2.0.tar.gz
Windows Binary	schex_1.2.0.zip
macOS 10.13 (High Sierra)	schex_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/schex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/schex
Package Short Url	https://bioconductor.org/packages/schex/
Package Downloads Report	Download Stats