supraHex

DOI: 10.18129/B9.bioc.supraHex    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see supraHex.

supraHex: a supra-hexagonal map for analysing tabular omics data

Bioconductor version: 3.12

A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics input data. The supraHex is able to carry out gene clustering/meta-clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. So with supraHex, it is also possible to carry out multilayer omics data comparisons. Newly added utilities are advanced heatmap visualisation and tree-based analysis of sample relationships. Uniquely to this package, users can ultrafastly understand any tabular omics data, both scientifically and artistically, especially in a sample-specific fashion but without loss of information on large genes.

Author: Hai Fang and Julian Gough

Maintainer: Hai Fang <hfang at well.ox.ac.uk>

Installation

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

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

BiocManager::install("supraHex")

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("supraHex")

 

PDF	R Script	supraHex User Manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GeneExpression, Software, Visualization
Version	1.28.2
In Bioconductor since	BioC 2.13 (R-3.0) (7.5 years)
License	GPL-2
Depends	R (>= 3.6), hexbin
Imports	ape, MASS, grDevices, graphics, stats, readr, tibble, tidyr, dplyr, stringr, purrr, magrittr, igraph, methods
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://suprahex.r-forge.r-project.org
Depends On Me	dnet
Imports Me	Pi
Suggests Me	TCGAbiolinks
Links To Me
Build Report

Package Archives

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

Source Package	supraHex_1.28.2.tar.gz
Windows Binary	supraHex_1.28.2.zip
macOS 10.13 (High Sierra)	supraHex_1.28.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/supraHex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/supraHex
Package Short Url	https://bioconductor.org/packages/supraHex/
Package Downloads Report	Download Stats