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supraHex specifications

Information


Unique identifier OMICS_04800
Name supraHex
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.7.3
Stability Stable
Requirements
hexbin
Maintained No

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Documentation


Additional information


http://supfam.org/supraHex/docs.html

Publication for supraHex

supraHex citations

 (3)
call_split

Nonpromoter methylation of the CDKN2A gene with active transcription is associated with improved locoregional control in laryngeal squamous cell carcinoma

2017
PMCID: 5313649
PMID: 28102032
DOI: 10.1002/cam4.961
call_split See protocol

[…] ylation levels (hypo‐ and hyper‐methylated) using Euclidean distance hierarchical clustering with complete linkage using all 4 CpG loci. The corresponding methylation heatmap was visualized using the supraHex v1.8.0 R package . To allow for statistical comparison, grouping of the TCGA samples was based on the distribution of M‐values for the single downstream CDKN2A CpG (cg12840719) assayed by the […]

library_books

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

2016
F1000Res
PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] 54 [37] IRanges _ 2.6.1 55 [38] S4Vectors _ 0.10.2 56 [39] lattice _ 0.20–33 57 [40] Biobase _ 2.32.0 58 [41] BiocGenerics _ 0.18.0 59 [42] ComplexHeatmap _ 1.10.2 60 [43] dnet _ 1.0.9 61 [44] supraHex _ 1.10.0 62 [45] hexbin _ 1.27.1 63 [46] igraph _ 1.0.1 64 [47] circlize _ 0.3.7 65 [48] pbapply _ 1.2–1 66 [49] gplots _ 3.0.1 67 [50] gaia _ 2.16.0 68 [51] readr _ 0.2.2 69 [52] dow […]

library_books

RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non immune pathways

2016
Sci Rep
PMCID: 5075905
PMID: 27774996
DOI: 10.1038/srep35671

[…] d the control group taking into account the paired design across the 3 cell lines, and used for further analysis. For gene clustering and visualization, the gene expression matrix was analyzed by the supraHex package. Genes with similar expression changes were self-organised onto nearby regions of a supra-hexagonal map. The resulting map was visualized to display sample-specific expression changes […]

Citations

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supraHex institution(s)
Computational Genomics Group, Department of Computer Science, University of Bristol, Bristol, UK
supraHex funding source(s)
Supported by the Biotechnology and Biological Sciences Research Council (BB/G022771/1).

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