Literature DB >> 22144163

Analyzing biological data using R: methods for graphs and networks.

Nolwenn Le Meur1, Robert Gentleman.   

Abstract

R is a powerful language and widely used software tool for the analysis and visualization of data. Its core capabilities can be extended through many different add-on packages. Among the many packages are some which offer a broad range of facilities for analyzing statistical properties of graphs. This chapter provides a practical tutorial covering the use of R methods for graphs and networks to examine biological data and analyze their topological and statistical properties.

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Year:  2012        PMID： 22144163     DOI： 10.1007/978-1-61779-361-5_19

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  12 in total

Review 1.  Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer.

Authors:  Tim N Beck; Adaeze J Chikwem; Nehal R Solanki; Erica A Golemis
Journal:  Physiol Genomics       Date:  2014-08-05       Impact factor: 3.107

2.  Expression differences between African American and Caucasian prostate cancer tissue reveals that stroma is the site of aggressive changes.

Authors:  Matthew A Kinseth; Zhenyu Jia; Farahnaz Rahmatpanah; Anne Sawyers; Manuel Sutton; Jessica Wang-Rodriguez; Dan Mercola; Kathleen L McGuire
Journal:  Int J Cancer       Date:  2013-07-13       Impact factor: 7.396

3.  RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.

Authors:  Mauro A A Castro; Xin Wang; Michael N C Fletcher; Kerstin B Meyer; Florian Markowetz
Journal:  Genome Biol       Date:  2012-04-24       Impact factor: 13.583

4.  ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

Authors:  Guipeng Li; Ming Li; Yiwei Zhang; Dong Wang; Rong Li; Roger Guimerà; Juntao Tony Gao; Michael Q Zhang
Journal:  PLoS One       Date:  2014-05-01       Impact factor: 3.240

Review 5.  Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data.

Authors:  Ivo D Dinov
Journal:  Gigascience       Date:  2016-02-25       Impact factor: 6.524

6.  Genome-wide analysis of auxin response factor gene family members in medicinal model plant Salvia miltiorrhiza.

Authors:  Zhichao Xu; Aijia Ji; Jingyuan Song; Shilin Chen
Journal:  Biol Open       Date:  2016-06-15       Impact factor: 2.422

7.  Inhibition of ALK1 signaling with dalantercept combined with VEGFR TKI leads to tumor stasis in renal cell carcinoma.

Authors:  Xiaoen Wang; Nicolas Solban; Prateek Khanna; Marcella Callea; Jiaxi Song; David C Alsop; R Scott Pearsall; Michael B Atkins; James W Mier; Sabina Signoretti; Marat Alimzhanov; Ravi Kumar; Manoj K Bhasin; Rupal S Bhatt
Journal:  Oncotarget       Date:  2016-07-05

Review 8.  The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate Cancer.

Authors:  Mark D Long; Dominic J Smiraglia; Moray J Campbell
Journal:  Biomolecules       Date:  2017-02-14

9.  RMol: a toolset for transforming SD/Molfile structure information into R objects.

Authors:  Martin Grabner; Kurt Varmuza; Matthias Dehmer
Journal:  Source Code Biol Med       Date:  2012-11-14

10.  BirdsEyeView (BEV): graphical overviews of experimental data.

Authors:  Lifeng Zhang; Daniel Berleant; Yi Wang; Ling Li; Diane Cook; Eve Syrkin Wurtele
Journal:  BMC Bioinformatics       Date:  2012-09-11       Impact factor: 3.169
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