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supraHex

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
supraHex User Manual PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, GeneExpression, Software, Visualization
Version 1.40.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2
Depends R (>= 3.6), hexbin
Imports ape, MASS, grDevices, graphics, stats, readr, tibble, tidyr, dplyr, stringr, purrr, magrittr, igraph, methods
System Requirements
URL http://suprahex.r-forge.r-project.org
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Suggests
Linking To
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Depends On Me
Imports Me Pi
Suggests Me OmnipathR, TCGAbiolinks
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Package Archives

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

Source Package supraHex_1.40.0.tar.gz
Windows Binary supraHex_1.40.0.zip
macOS Binary (x86_64) supraHex_1.40.0.tgz
macOS Binary (arm64) supraHex_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/supraHex
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/supraHex
Bioc Package Browser https://code.bioconductor.org/browse/supraHex/
Package Short Url https://bioconductor.org/packages/supraHex/
Package Downloads Report Download Stats