schex

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see schex.

Hexbin plots for single cell omics data

Bioconductor version: 3.21

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. 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 [aut, cre], Wancheng Tang [ctb], Zimo Peng [ctb], Jingxiu Huang [ctb]

Maintainer: Saskia Freytag <freytag.s at wehi.edu.au>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")

Seurat_to_SCE HTML R Script

using_schex HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DimensionReduction, ImmunoOncology, Sequencing, SingleCell, Software, Visualization

Version 1.22.0

In Bioconductor since BioC 3.10 (R-3.6) (6 years)

License GPL-3

Depends SingleCellExperiment(>= 1.7.4), ggplot2 (>= 3.2.1)

Imports hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman

System Requirements

URL https://github.com/SaskiaFreytag/schex

Bug Reports https://github.com/SaskiaFreytag/schex/issues

Suggests ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle

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_1.22.0.tar.gz

Windows Binary (x86_64) schex_1.22.0.zip

macOS Binary (x86_64) schex_1.22.0.tgz

macOS Binary (arm64) schex_1.22.0.tgz

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