ndexr—an R package to interface with the network data exchange

Auer, Florian; Hammoud, Zaynab; Ishkin, Alexandr; Pratt, Dexter; Ideker, Trey

doi:10.1093/bioinformatics/btx683

Cited by 13 publications

(11 citation statements)

References 8 publications

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“…As this format becomes one of the standards to exchange graphs, we believe that it is essential to include it in our package. The converter provided by mully aims to export mully graphs in a CX format by using the RCX/ndexr R package [ 8 ]. By exporting the graph as a CX object, the user can then import it and use it into other tools supporting the CX format such as Cytoscape.…”

Section: Results and Featuresmentioning

confidence: 99%

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mully: An R Package to Create, Modify and Visualize Multilayered Graphs

Hammoud

2018

Genes

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The modelling of complex biological networks such as pathways has been a necessity for scientists over the last decades. The study of these networks also imposes a need to investigate different aspects of nodes or edges within the networks, or other biomedical knowledge related to it. Our aim is to provide a generic modelling framework to integrate multiple pathway types and further knowledge sources influencing these networks. This framework is defined by a multi-layered model allowing automatic network transformations and documentation. By providing a tool that generates this model, we aim to facilitate the data integration, boost the reproducibility and increase the interoperability between different sources and databases in the field of pathways. We present mully R package that allows the user to create, modify and visualize graphs with multi-layers. The package is implemented with features to specifically handle multilayered graphs.

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Section: Results and Featuresmentioning

confidence: 99%

“…It uses functions from other packages, for instance the 3D visualization is generated using the rgl R package [ 7 ], with some modifications applied concerning the layouting. It also refers to the RCX/ndexr package [ 8 ] to export the mully graph in Cytoscape Cyberinfrastructure Network Interchange Format (CX) [ 9 ] using its constructor.…”

Section: Methodsmentioning

confidence: 99%

mully: An R Package to Create, Modify and Visualize Multilayered Graphs

Hammoud

2018

Genes

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“… [ 71 ] PSICQUIC [ 120 ] Cytoscape Cyberinfrastructure Network Interchange Format (CX) A light weight REST-based aspect-oriented interchange protocol for generic network data exchange. [ 121 ] [ 122 ] …”

Section: Description Of Current Tools For Systems Medicine In Cardiovmentioning

confidence: 99%

New perspectives: systems medicine in cardiovascular disease

Just

Zeller²

2018

BMC Syst Biol

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BackgroundCardiovascular diseases (CVD) represent one of the most important causes of morbidity and mortality worldwide. Innovative approaches to increase the understanding of the underpinnings of CVD promise to enhance CVD risk assessment and might pave the way to tailored therapies. Within the last years, systems medicine has emerged as a novel tool to study the genetic, molecular and physiological interactions.ConclusionIn this review, we provide an overview of the current molecular-experimental, epidemiological and bioinformatical tools applied in systems medicine in the cardiovascular field. We will discuss the status and challenges in implementing interdisciplinary systems medicine approaches in CVD.

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“…To illustrate this, we performed Pearson correlation analysis across the DMGs in all of the cancers in our database, retaining gene pairs with P < 0.01, cor > 0.6 to form a co-methylation network of 31 cancers, respectively. The modules were mined using the R package ‘igraph’ ( 38 ). Due to limitations of picture clarity using a network module with an excess of genes, only the top 250 relationship pairs with the largest correlation coefficient are displayed.…”

Section: Introductionmentioning

confidence: 99%

DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database

Xing

Zhai

Liu

et al. 2021

Nucleic Acids Research

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DNA methylation has a growing potential for use as a biomarker because of its involvement in disease. DNA methylation data have also substantially grown in volume during the past 5 years. To facilitate access to these fragmented data, we proposed DiseaseMeth version 3.0 based on DiseaseMeth version 2.0, in which the number of diseases including increased from 88 to 162 and High-throughput profiles samples increased from 32 701 to 49 949. Experimentally confirmed associations added 448 pairs obtained by manual literature mining from 1472 papers in PubMed. The search, analyze and tools sections were updated to increase performance. In particular, the FunctionSearch now provides for the functional enrichment of genes from localized GO and KEGG annotation. We have also developed a unified analysis pipeline for identifying differentially DNA methylated genes (DMGs) from the original data stored in the database. 22 718 DMGs were found in 99 diseases. These DMGs offer application in disease evaluation using two self-developed online tools, Methylation Disease Correlation and Cancer Prognosis & Co-Methylation. All query results can be downloaded and can also be displayed through a box plot, heatmap or network module according to whichever search section is used. DiseaseMeth version 3.0 is freely available at http://diseasemeth.edbc.org/.

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ndexr—an R package to interface with the network data exchange

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 13 publications

References 8 publications

mully: An R Package to Create, Modify and Visualize Multilayered Graphs

mully: An R Package to Create, Modify and Visualize Multilayered Graphs

New perspectives: systems medicine in cardiovascular disease

DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database

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