Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: RCy3
https://packages.ecosyste.ms/registries/bioconductor.org/packages/RCy3
Functions to Access and Control Cytoscape
1 version
Latest release: about 1 year ago
14 dependent packages
63,728 downloads total
Papers Mentioning RCy3 22
10.1371/journal.pone.0248185
Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and BlastocystisCited by: 15
Author(s): Laura Vega, Giovanny Herrera, Marina Muñoz, Manuel A. Patarroyo, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 14
Published: almost 4 years ago
10.1186/s13059-019-1851-8
Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancerCited by: 44
Author(s): Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth, Melissa J. Davis
Software Mentions: 14
Published: about 5 years ago
10.3390/ijerph18094859
A Network Approach for the Study of Drug Prescriptions: Analysis of Administrative Records from a Local Health Unit (ASL TO4, Regione Piemonte, Italy)Cited by: 2
Author(s): Gianluca Miglio, Lara Denise Basso, Lucrezia Greta Armando, Sara Traina, Elisa Benetti, Abdoulaye Diarassouba, Raffaella Baroetto Parisi, Mariangela Esiliato, Cristina Rolando, Elisa Remani, Clara Cena
Software Mentions: 12
Published: over 3 years ago
10.7554/eLife.69040
Common virulence gene expression in adult first-time infected malaria patients and severe casesCited by: 15
Author(s): Jan Stephan Wichers, Gerry Tonkin‐Hill, Thorsten Thye, Ralf Krumkamp, Benno Kreuels, Jan Strauss, Heidrun von Thien, Jochen Scholz, Helle Hansson, Rasmus Weisel Jensen, Louise Turner, Freia-Raphaella Lorenz, Anna Schöllhorn, Iris Bruchhaus, Egbert Tannich, Rolf Fendel, Thomas D. Otto, Thomas Lavstsen, Tim‐Wolf Gilberger, Michael Duffy, Anna Bachmann
Software Mentions: 9
Published: over 3 years ago
10.1186/s12864-021-07918-2
CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysisCited by: 10
Author(s): Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson A. Silva
Software Mentions: 8
Published: over 3 years ago
10.12688/f1000research.6767.1
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful APICited by: 77
Author(s): Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak
Software Mentions: 8
Published: over 9 years ago
10.12688/f1000research.20887.3
RCy3: Network biology using Cytoscape from within RCited by: 72
Author(s): Julia Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Software Mentions: 6
Published: about 5 years ago
10.1371/journal.pcbi.1008685
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathwaysCited by: 9
Author(s): Agatha Treveil, Balázs Bohár, Padhmanand Sudhakar, Lejla Gul, Luca Csabai, Márton Ölbei, Martina Poletti, Matthew Madgwick, Tahila Andrighetti, Isabelle Hautefort, Dezső Módos, Tamás Korcsmáros
Software Mentions: 6
Published: almost 4 years ago
10.3389/fnut.2021.675935
Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose TissueCited by: 1
Author(s): Marianthi Kalafati, Michael Lenz, Gökhan Ertaylan, Ilja C. W. Arts, Chris T. Evelo, Marleen M.J. van Greevenbroek, Ellen E. Blaak, Michiel E. Adriaens, Martina Kutmon
Software Mentions: 5
Published: over 3 years ago
10.3390/metabo10020066
EFMviz: A COBRA Toolbox Extension to Visualize Elementary Flux Modes in Genome-Scale Metabolic ModelsCited by: 6
Author(s): Chaitra Sarathy, Martina Kutmon, Michael Lenz, Michiel E. Adriaens, Chris T. Evelo, Ilja C. W. Arts
Software Mentions: 5
Published: almost 5 years ago
10.3390/genes11070831
Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene NetworksCited by: 5
Author(s): Fernando M. Delgado-Chaves, Francisco Gómez-Vela, Federico Divina, Miguel García-Torres, Domingo S. Rodríguez–Baena
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-020-80093-8
An enriched biosignature of gut microbiota-dependent metabolites characterizes maternal plasma in a mouse model of fetal alcohol spectrum disorderCited by: 20
Author(s): Manjot S Virdee, Nipun Saini, Colin D. Kay, Andrew P. Neilson, Sze Ting Cecilia Kwan, Kaylee K. Helfrich, Sandra M. Mooney, Susan Smith
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41398-020-0776-z
Elevated serum chemokine CCL22 levels in first-episode psychosis: associations with symptoms, peripheral immune state and in vivo brain glial cell functionCited by: 14
Author(s): Heikki Laurikainen, Arja Vuorela, Anna Toivonen, Linnea Reinert-Hartwall, Kalevi Trontti, Maija Lindgren, Jaakko Keinänen, Teemu Mäntylä, Janina Paju, Tuula Ilonen, Reetta-Liina Armio, Maija Walta, Jouni Tuisku, Semi Helin, Päivi Marjamäki, Iiris Hovatta, Sebastian Therman, Outi Vaarala, Outi Linnaranta, Tuula Kieseppä, Raimo K. R. Salokangas, Jarno Honkanen, Jarmo Hietala, Jaana Suvisaari
Software Mentions: 4
Published: almost 5 years ago
10.12688/f1000research.26429.2
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networksCited by: 2
Author(s): Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Manjool Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach, Gary D. Bader
Software Mentions: 4
Published: almost 4 years ago
10.1186/s13059-019-1758-4
Cytoscape Automation: empowering workflow-based network analysisCited by: 753
Author(s): David Otasek, John H. Morris, Jorge Bouças, Alexander Pico, Barry Demchak
Software Mentions: 4
Published: over 5 years ago
10.1038/s41598-020-67588-0
Glomerular endothelial cell heterogeneity in Alport syndromeCited by: 8
Author(s): Hasmik Soloyan, Matthew E. Thornton, Valentina Villani, Patrick Khatchadourian, Paolo Cravedi, Andrea Angeletti, Brendan H. Grubbs, Roger De Filippo, Laura Perin, Sargis Sedrakyan
Software Mentions: 3
Published: over 4 years ago
10.7717/peerj.11121
Network based multifactorial modelling of miRNA-target interactionsCited by: 1
Author(s): Selcen Arı Yuka, Alper Yılmaz
Software Mentions: 3
Published: almost 4 years ago
10.12688/f1000research.14612.2
eXamine: Visualizing annotated networks in CytoscapeCited by: 3
Author(s): Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir
Software Mentions: 3
Published: over 6 years ago
10.1038/s42003-021-01822-x
Expanding the drug discovery space with predicted metabolite–target interactionsCited by: 8
Author(s): Andrea Nuzzo, Somdutta Saha, Ellen L. Berg, Channa Jayawickreme, Joel Tocker, James R. Brown
Software Mentions: 2
Published: almost 4 years ago
10.12688/f1000research.14616.1
Automating the PathLinker app for CytoscapeCited by: 9
Author(s): Li Jun Huang, Jeffrey Law, T. M. Murali
Software Mentions: 2
Published: over 6 years ago
10.12688/f1000research.22280.2
Visualize omics data on networks with Omics Visualizer, a Cytoscape AppCited by: 30
Author(s): Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen
Software Mentions: 2
Published: over 4 years ago
10.12688/f1000research.14807.2
Identifier Mapping in CytoscapeCited by: 7
Author(s): Adam Treister, Alexander R. Pico
Software Mentions: 2
Published: over 6 years ago