supraHex

A supra-hexagonal map for analysing tabular omics data

Bioconductor version: Development (3.0)

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 (see http://www.ncbi.nlm.nih.gov/pubmed/24309102).

Author: Hai Fang and Julian Gough

Maintainer: Hai Fang <hfang at cs.bris.ac.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("supraHex")

To cite this package in a publication, start R and enter:

    citation("supraHex")

Documentation

PDF R Script supraHex User Manual
PDF   Reference Manual
Text   NEWS

Details

biocViews Bioinformatics, Clustering, GeneExpression, Software, Visualization
Version 1.3.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-2
Depends R (>= 3.0.2), hexbin
Imports ape, MASS
Suggests
System Requirements
URL http://supfam.org/supraHex
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source supraHex_1.3.0.tar.gz
Windows Binary supraHex_1.3.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) supraHex_1.3.0.tgz
Mac OS X 10.9 (Mavericks)
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