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schex

This is the development version of schex; for the stable release version, see schex.

Hexbin plots for single cell omics data


Bioconductor version: Development (3.19)

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>

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

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

Details

biocViews DimensionReduction, Sequencing, SingleCell, Software, Visualization
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
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
System Requirements
URL https://github.com/SaskiaFreytag/schex
Bug Reports https://github.com/SaskiaFreytag/schex/issues
See More
Suggests ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran
Linking To
Enhances
Depends On Me
Imports Me scTensor, scTGIF
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package schex_1.17.0.tar.gz
Windows Binary schex_1.17.0.zip
macOS Binary (x86_64) schex_1.17.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/schex
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/schex
Bioc Package Browser https://code.bioconductor.org/browse/schex/
Package Short Url https://bioconductor.org/packages/schex/
Package Downloads Report Download Stats