bioconductor: Rgraphviz | Projects

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: over 10 years ago

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: about 11 years ago

10.1186/gb-2004-5-10-r80

Cited by: 10,848
Author(s): Robert Gentleman, Vincent J. Carey, Douglas M. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Maria Iacus, Rafael A. Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony Rossini, Günther Sawitzki, Colin A. Smith, Gordon K. Smyth, Luke Tierney, Jean Yee Hwa Yang, Jianhua Zhang
Software Mentions: 10
Published: almost 21 years ago

10.1186/s12863-015-0190-3

strum: an R package for structural modeling of latent variables for general pedigrees
Cited by: 6
Author(s): Yeunjoo E. Song, Catherine M. Stein, Nathan Morris
Software Mentions: 9
Published: over 9 years ago

10.1093/bioinformatics/btw763

ontologyX: a suite of R packages for working with ontological data
Cited by: 66
Author(s): Daniel Greene, Sylvia Richardson, Ernest Turro
Software Mentions: 9
Published: almost 8 years ago

10.18632/oncotarget.13467

Effects of Abies sibirica terpenes on cancer- and aging-associated pathways in human cells
Cited by: 9
Author(s): Anna V. Kudryavtseva, George S. Krasnov, Anastasiya V. Lipatova, B. Ya. Alekseev, Faniya Maganova, Mikhail Shaposhnikov, Maria S. Fedorova, Anastasiya V. Snezhkina, Alexey Moskalev
Software Mentions: 8
Published: almost 8 years ago

10.18632/oncotarget.16664

MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing
Cited by: 31
Author(s): Ugnė Gyvytė, Simonas Juzėnas, Violeta Šaltenienė, Juozas Kupčinskas, Lina Poškienė, Laimutis Kučinskas, Sonata Jarmalaitė, Kristina Stuopelytė, Rūta Steponaitienė, Georg Hemmrich-Stanisak, Matthias Hübenthal, Alexander Link, Sabine Franke, André Franke, Dalia Pangonytė, Vaiva Lesauskaitė, Limas Kupčinskas, Jurgita Skiecevičienė
Software Mentions: 8
Published: over 7 years ago

10.1186/1471-2105-14-179

Modelling and visualizing fine-scale linkage disequilibrium structure
Cited by: 3
Author(s): D.J. Edwards
Software Mentions: 8
Published: over 11 years ago

10.1186/1471-2105-8-S6-S8

Graphs in molecular biology
Cited by: 108
Author(s): Wolfgang Huber, Vincent J. Carey, Long Li, Seth Falcon, Robert Gentleman
Software Mentions: 7
Published: about 17 years ago

10.1186/s12864-019-6155-6

A framework using topological pathways for deeper analysis of transcriptome data
Cited by: 0
Author(s): Yue Zhao, Stephanie Piekos, Tham H. Hoang, Dong-Guk Shin
Software Mentions: 7
Published: over 4 years ago

10.1186/gb-2012-13-4-r29

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.
Cited by: 84
Author(s): Mauro A. A. Castro, Xin Wang, Michael Fletcher, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 7
Published: almost 13 years ago

10.1038/s41598-021-84995-z

Genetic co-expression networks contribute to creating predictive model and exploring novel biomarkers for the prognosis of breast cancer
Cited by: 1
Author(s): Yuan-Kuei Li, Huan-Ming Hsu, Meng-Chiung Lin, Chi‐Wen Chang, Chi‐Ming Chu, Yu‐Jia Chang, Jyh‐Cherng Yu, Chien-Ting Chen, Chen-En Jian, Chien‐An Sun, Kanghua Chen, Ming-Hao Kuo, Chia-Shiang Cheng, Ya-Ting Chang, Yi-Syuan Wu, Hao-Yi Wu, Yating Yang, Chen Lin, Hung‐Che Lin, Je-Ming Hu, Yu-Tien Chang
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-94628-0

Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning
Cited by: 5
Author(s): Heyang Yuan, Xuehao Wang, Tzu-Yu Lin, Jinha Kim, Wen Tso Liu
Software Mentions: 4
Published: about 3 years ago

10.1186/1475-2859-8-37

Interactive visualization of clusters in microarray data: an efficient tool for improved metabolic analysis of E. coli
Cited by: 7
Author(s): Theresa Scharl, Gerald Striedner, Florentina Pötschacher, Friedrich Leisch, Karl Bayer
Software Mentions: 4
Published: about 15 years ago

10.1186/1471-2105-9-461

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information
Cited by: 469
Author(s): Patrick Meyer, Frédéric Lafitte, Gianluca Bontempi
Software Mentions: 4
Published: almost 16 years ago

10.1186/1471-2105-10-288

Exploratory and inferential analysis of gene cluster neighborhood graphs
Cited by: 4
Author(s): Theresa Scharl, Ingo Voglhuber, Friedrich Leisch
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2105-8-166

GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products
Cited by: 178
Author(s): Holger Fröhlich, N. Speer, Annemarie Poustka, Tim Beißbarth
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2164-13-623

High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome
Cited by: 46
Author(s): Danni Yu, John Danku, Ivan Baxter, Sungjin Kim, Olena K. Vatamaniuk, Olga Vitek, Mourad Ouzzani, David E. Salt
Software Mentions: 3
Published: almost 12 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.ppat.1001074

Global Genotype-Phenotype Correlations in Pseudomonas aeruginosa
Cited by: 11
Author(s): Claudia Pommerenke, Mathias Müsken, Tanja Becker, Andreas Dötsch, Frank Klawonn, Susanne Häußler
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.ppat.1003081

Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks
Cited by: 57
Author(s): Joseph Hughes, Richard C. Allen, Marc Baguelin, Katie Hampson, Gregory J. Baillie, Debra Elton, J. R. Newton, Paul Kellam, James Wood, Edward C. Holmes, Pablo R. Murcia
Software Mentions: 3
Published: almost 12 years ago

10.7150/ijbs.40173

Knockdown of SMAD3 inhibits the growth and enhances the radiosensitivity of lung adenocarcinoma via p21 in vitro and in vivo
Cited by: 22
Author(s): Hao Niu, Yiwei Huang, Yan Li, Li Zhang, Mengnan Zhao, Tao Lu, Xiaodong Yang, Zhengcong Chen, Cheng Zhan, Yu Shi, Qun Wang
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0085256

Online Respondent-Driven Sampling for Studying Contact Patterns Relevant for the Spread of Close-Contact Pathogens: A Pilot Study in Thailand
Cited by: 36
Author(s): Mart L. Stein, Jim E. van Steenbergen, Charnchudhi Chanyasanha, Mathuros Tipayamongkholgul, Vincent Buskens, P.G.M. van der Heijden, Wasamon Sabaiwan, Linus Bengtsson, Xin Lu, Anna Thorson, Mirjam Kretzschmar
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-11-214

Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
Cited by: 38
Author(s): Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Mizutani, Kazuki Saito, Masanori Arita
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-11-S9-S11

Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models
Cited by: 4
Author(s): Xinan Yang, Younghee Lee, Yong Huang, James L. Chen, Rosie Hongmei Xing, Yves A. Lussier
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0073445

Topographical Body Fat Distribution Links to Amino Acid and Lipid Metabolism in Healthy Non-Obese Women
Cited by: 35
Author(s): François-Pierre Martin, Ivan Montoliu, Sebastiano Collino, Max Scherer, Philippe A. Guy, Isabelle Tavazzi, Anita Thorimbert, Sofia Moco, Megan P. Rothney, David L. Ergun, Maurice Beaumont, Fiona Ginty, Salah D. Qanadli, Lucie Favre, Vittorio Giusti, Serge Rezzi
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0056564

Metabolic Signatures of Extreme Longevity in Northern Italian Centenarians Reveal a Complex Remodeling of Lipids, Amino Acids, and Gut Microbiota Metabolism
Cited by: 181
Author(s): Sebastiano Collino, Ivan Montoliu, François‐Pierre J. Martin, Max Scherer, Daniela Mari, Stefano Salvioli, Laura Bucci, Rita Ostan, Daniela Monti, Elena Biagi, Patrizia Brigidi, Claudio Franceschi, Serge Rezzi
Software Mentions: 2
Published: over 11 years ago

10.1186/gb-2010-11-11-r115

Constructing a fish metabolic network model
Cited by: 42
Author(s): Shuzhao Li, Alex Pozhitkov, Rachel A. Ryan, C. Steve Manning, Nancy J. Brown‐Peterson, Marius Brouwer
Software Mentions: 2
Published: almost 15 years ago

10.3390/cells9071697

In Silico Evaluation of Putative S100B Interacting Proteins in Healthy and IBD Gut Microbiota
Cited by: 8
Author(s): Massimiliano Orsini, Rosa Di Liddo, Federica Valeriani, Marzia Mancin, R. D’Incà, Andréa Castagnetti, Antonio Aceti, Pier Paolo Parnigotto, Vincenzo Romano Spica, Fabrizio Michetti
Software Mentions: 2
Published: about 4 years ago

10.1038/s41398-019-0373-1

Stress dynamically regulates co-expression networks of glucocorticoid receptor-dependent MDD and SCZ risk genes
Cited by: 9
Author(s): Corinna Zimmermann, Janine Arloth, Sara Santarelli, Anne Löschner, Peter Weber, Mathias Schmidt, Dietmar Spengler, Elisabeth B. Binder
Software Mentions: 2
Published: over 5 years ago

10.1186/s12863-016-0440-z

Genetic signals of high-altitude adaptation in amphibians: a comparative transcriptome analysis
Cited by: 17
Author(s): Weizhao Yang, Yin Qi, Jinzhong Fu
Software Mentions: 1
Published: about 8 years ago

10.3389/fimmu.2015.00428

Differential Expression of microRNAs in Thymic Epithelial Cells from Trypanosoma cruzi Acutely Infected Mice: Putative Role in Thymic Atrophy
Cited by: 33
Author(s): Leandra Linhares-Lacerda, Cintia Palu, Marcelo Ribeiro-Alves, Bruno Diaz Paredes, Alexandre Morrot, María Rosa García-Silva, Alfonso Cayota, Wilson Savino
Software Mentions: 1
Published: about 9 years ago

Ecosyste.ms: Papers

Projects: bioconductor: Rgraphviz

Papers Mentioning Rgraphviz 33