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schex

Hexbin plots for single cell omics data


Bioconductor version: Release (3.18)

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 [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 "4.3") 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

Details

biocViews DataImport, DimensionReduction, ImmunoOncology, Sequencing, SingleCell, Software, Visualization
Version 1.16.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
See More
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 fcoex
Links To Me
Build Report Build Report

Package Archives

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

Source Package schex_1.16.1.tar.gz
Windows Binary schex_1.16.1.zip (64-bit only)
macOS Binary (x86_64) schex_1.16.1.tgz
macOS Binary (arm64) schex_1.16.1.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
Old Source Packages for BioC 3.18 Source Archive