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Home @ supraHex 1.10.1

SupraHex 1.10.1. An open-source R/Bioconductor package for tabular omics data analysis using. The artwork called supraHex. Has won The Best Artwork Award in ISMB 2014. This artwork is automatically done and is reproducible here. Demonstrated in a variety of genome-wide datasets such as:. And clonal population structure. Is a giant hexagon on a 2-dimensional map grid seamlessly consisting of smaller hexagons. For more, see slides. And poster in ISMB2014. Visualisations at and across nodes of the map;.

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Home @ supraHex 1.10.1 | suprahex.r-forge.r-project.org Reviews

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SupraHex 1.10.1. An open-source R/Bioconductor package for tabular omics data analysis using. The artwork called supraHex. Has won The Best Artwork Award in ISMB 2014. This artwork is automatically done and is reproducible here. Demonstrated in a variety of genome-wide datasets such as:. And clonal population structure. Is a giant hexagon on a 2-dimensional map grid seamlessly consisting of smaller hexagons. For more, see slides. And poster in ISMB2014. Visualisations at and across nodes of the map;.

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1 documentations

2 installation

3 demos

4 faqs

5 citation

6 a supra hexagonal map

7 news

8 leukemia patient transcriptome

9 time course transcriptome

10 rna seq data

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Home @ supraHex 1.10.1 | suprahex.r-forge.r-project.org Reviews

https://suprahex.r-forge.r-project.org

SupraHex 1.10.1. An open-source R/Bioconductor package for tabular omics data analysis using. The artwork called supraHex. Has won The Best Artwork Award in ISMB 2014. This artwork is automatically done and is reproducible here. Demonstrated in a variety of genome-wide datasets such as:. And clonal population structure. Is a giant hexagon on a 2-dimensional map grid seamlessly consisting of smaller hexagons. For more, see slides. And poster in ISMB2014. Visualisations at and across nodes of the map;.

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suprahex.r-forge.r-project.org

1

Docs @ supraHex 1.10.1

http://suprahex.r-forge.r-project.org/docs.html

SupraHex 1.10.1. Training and Analysis functions. These functions are used for training and analysis. Function to setup the pipeline for completing ab initio training given the input data. Function to define a supra-hexagonal grid. Function to define the topology of a map grid. Function to initialise a sInit object given a topology and input data. Function to define trainology (training environment). Function to implement training via sequential algorithm. Function to partition a grid map into clusters.

2

FAQs @ supraHex 1.10.1

http://suprahex.r-forge.r-project.org/faqs.html

SupraHex 1.10.1. What is the supra-hexagonal map? How to control the layout when using visCompReorder? How to control the device output generated by visCompReorder? Does visDmatCluster serve as a gene cluster legend to the samples visualised by visCompReorder? How to add a legend key to visDmatCluster? How to choose the training algorithm: sequential vs batch? How many neighborhood kernels are supported and how to choose?

3

Demo for for the artwork in ISMB 2014 @ supraHex 1.10.1

http://suprahex.r-forge.r-project.org/demo-ISMB2014.html

SupraHex 1.10.1. Demo for for the artwork in ISMB 2014. All results are based on supraHex (version 1.10.1). R scripts (i.e. R expressions) plus necessary comments are highlighted in light cyan, and the rest are outputs in the screen. Images displayed below may be distorted, but should be normal in your screen. Functions contained in supraHex 1.10.1 are hyperlinked in-place and also listed on the right side. Loading required package: Biobase. Loading required package: BiocGenerics. Preprocess data (this s...

4

Cite @ supraHex 1.10.1

http://suprahex.r-forge.r-project.org/cite.html

SupraHex 1.10.1. Fang H, Gough J. (2014) supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map. Biochemical and Biophysical Research Communications. 443(1), 285-289. doi:10.1016/j.bbrc.2013.11.103. Computational Genomics Group, Department of Computer Science, University of Bristol, UK.

5

Demos @ supraHex 1.10.1

http://suprahex.r-forge.r-project.org/demos.html

SupraHex 1.10.1. Demo for multilayer omics dataset from Hiratani et al. Demo for leukemia patient dataset from Golub et al. Demo for human embryo dataset from Fang et al. Demo for arabidopsis embryo dataset from Xiang et al. Demo for for the artwork in ISMB 2014. Demo for human cell type evolutionary profile dataset from Sardar et al. Demo for postprocessing cellular prevalence of mutations in clonal populations (inferred by PyClone). Demo for analysing RNA-seq dataset (along with edgeR).

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supfam.org

Home @ supraHex 1.7.3

http://supfam.org/supraHex

SupraHex 1.7.3. An open-source R/Bioconductor package for tabular omics data analysis using. The artwork called supraHex. Has won The Best Artwork Award in ISMB 2014. This artwork is automatically done and is reproducible here. Demonstrated in a variety of genome-wide datasets such as:. And clonal population structure. Is a giant hexagon on a 2-dimensional map grid seamlessly consisting of smaller hexagons. For more, see slides. And poster in ISMB2014. Visualisations at and across nodes of the map;.

r-forge.r-project.org

R-Forge: supraHex: Project Home

https://r-forge.r-project.org/projects/suprahex

Search the entire project. SupraHex: Project Home R-Forge. SupraHex devises a supra-hexagonal map, a giant hexagon on a 2D map grid consisting of smaller hexagons, for self-organising tabular omics data, carrying out gene clustering, sample correlation and multilayer omics data comparisons. GNU General Public License (GPL). View list of RSS feeds. Available for this project. 0 Comment Read More/Comment.

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suprahex.r-forge.r-project.org

Home @ supraHex 1.10.1

SupraHex 1.10.1. An open-source R/Bioconductor package for tabular omics data analysis using. The artwork called supraHex. Has won The Best Artwork Award in ISMB 2014. This artwork is automatically done and is reproducible here. Demonstrated in a variety of genome-wide datasets such as:. And clonal population structure. Is a giant hexagon on a 2-dimensional map grid seamlessly consisting of smaller hexagons. For more, see slides. And poster in ISMB2014. Visualisations at and across nodes of the map;.

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