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Dnet 1.0.7. An open-source R package for omics data integrative analysis in terms of. Identification of gene-active networks from high-throughput omics data (e.g. mutation. Network-based sample classifications and visualisations on 2D sample landscape;. Random Walk with Restart for network affinity calculation;. Semantic similarity between ontology terms (and between their annotated genes);. Enrichment analysis using a variety of built-in databases;. A wide variety of built-in RData.

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Home @ dnet 1.0.7 | dnet.r-forge.r-project.org Reviews

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Dnet 1.0.7. An open-source R package for omics data integrative analysis in terms of. Identification of gene-active networks from high-throughput omics data (e.g. mutation. Network-based sample classifications and visualisations on 2D sample landscape;. Random Walk with Restart for network affinity calculation;. Semantic similarity between ontology terms (and between their annotated genes);. Enrichment analysis using a variety of built-in databases;. A wide variety of built-in RData.

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1 installation

2 documentations

3 rdata

4 demos

5 faqs

6 citation

7 network

8 evolution

9 ontology

10 user i/o

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Home @ dnet 1.0.7 | dnet.r-forge.r-project.org Reviews

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

Dnet 1.0.7. An open-source R package for omics data integrative analysis in terms of. Identification of gene-active networks from high-throughput omics data (e.g. mutation. Network-based sample classifications and visualisations on 2D sample landscape;. Random Walk with Restart for network affinity calculation;. Semantic similarity between ontology terms (and between their annotated genes);. Enrichment analysis using a variety of built-in databases;. A wide variety of built-in RData.

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dnet.r-forge.r-project.org

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Demo for patient expression dataset @ dnet 1.0.7

http://dnet.r-forge.r-project.org/demo-CLL.html

Dnet 1.0.7. Demo for patient expression dataset. All results are based on dnet (version 1.0.7). 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 dnet 1.0.7 are hyperlinked in-place and also listed on the right side. Require(pkg, character.only=T) { source("http:/ bioconductor.org/biocLite.R") biocLite(pkg) lapply(pkg,...Non-speci...

2

FAQs @ dnet 1.0.7

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

Dnet 1.0.7. How to obtain the dnet package and what it can do? What is the built-in data and how to use? How to obtain a list of genes with significance information that can be used for identifying gene-active networks? How many ways are supported to visualise gene-active networks? What is Random Walk with Restart (RWR)? How to extract a subnetwork that revolves around a specific gene of interest? Computational Genomics Group, Department of Computer Science, University of Bristol, UK.

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Install @ dnet 1.0.7

http://dnet.r-forge.r-project.org/install.html

Dnet 1.0.7. R ( http:/ www.r-project.org. Is a language and environment for statistical computing and graphics. We assume R (version 3.1.0 or higher) has been installed in your local machine. The latest version can be installed following instructions below for different platforms (Windows, Mac, and Linux). Download R for Windows. Download R for Mac OS X 10.6 (Snow Leopard or higher). Shell command lines in Terminal. Assume you have a. 2 Installation of the package. Second, install the package. Library(de...

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Home @ dnet 1.0.7

http://dnet.r-forge.r-project.org/index.html

Dnet 1.0.7. An open-source R package for omics data integrative analysis in terms of. Identification of gene-active networks from high-throughput omics data (e.g. mutation. Network-based sample classifications and visualisations on 2D sample landscape;. Random Walk with Restart for network affinity calculation;. Semantic similarity between ontology terms (and between their annotated genes);. Enrichment analysis using a variety of built-in databases;. A wide variety of built-in RData.

5

Demos @ dnet 1.0.7

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

Dnet 1.0.7. Demo for TCGA mutation and survival dataset. Demo for multilayer replication timing dataset. Demo for patient expression dataset. Demo for time-course expression dataset. Computational Genomics Group, Department of Computer Science, University of Bristol, UK.

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bioinformatics.bris.ac.uk

Software - Computational Genomics Group

http://www.bioinformatics.bris.ac.uk/software.html

The Mogrify resource predicts how to trans-differentiation from any human cell type to any other human cell typeby perturbing the transcriptional network. Mogrify includes all cell types from the FANTOM5. Database contains assignments of protein domains of known structures to all completely sequenced genomes. The library of hidden Markov models and the software required to run the SUPERFAMILY assignment procedure is available from the downloads page. There is a very low traffic mailing list. A community ...

simkes2012.wordpress.com

simkesUGM2012 | Catatan Mahasiswa SIMKES UGM 2012 | Page 2

https://simkes2012.wordpress.com/page/2

Catatan Mahasiswa SIMKES UGM 2012. April 10, 2014. List of open-source bioinformatics software. From : http:/ en.wikipedia.org/wiki/List of open source bioinformatics software. A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists. GNU General Public License. Framework for data analysis. Tool for designing and executing phylogenetic workflows. General Public Licence (GPL). Suite of automated docking tools. 50,90,100), RefSeq.

bioinformatics.bristol.ac.uk

Software - Computational Genomics Group

http://www.bioinformatics.bristol.ac.uk/software.html

The Mogrify resource predicts how to trans-differentiation from any human cell type to any other human cell typeby perturbing the transcriptional network. Mogrify includes all cell types from the FANTOM5. Database contains assignments of protein domains of known structures to all completely sequenced genomes. The library of hidden Markov models and the software required to run the SUPERFAMILY assignment procedure is available from the downloads page. There is a very low traffic mailing list. A community ...

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Home @ dnet 1.0.7

Dnet 1.0.7. An open-source R package for omics data integrative analysis in terms of. Identification of gene-active networks from high-throughput omics data (e.g. mutation. Network-based sample classifications and visualisations on 2D sample landscape;. Random Walk with Restart for network affinity calculation;. Semantic similarity between ontology terms (and between their annotated genes);. Enrichment analysis using a variety of built-in databases;. A wide variety of built-in RData.

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