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

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis
Cited 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: over 3 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 cancer
Cited 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 cases
Cited 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) analysis
Cited 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 API
Cited 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 R
Cited by: 72
Author(s): Julia Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Software Mentions: 6
Published: almost 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 pathways
Cited 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 Tissue
Cited 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 Models
Cited 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 Networks
Cited 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 disorder
Cited 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 function
Cited 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: over 4 years ago

10.12688/f1000research.26429.2

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
Cited 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 analysis
Cited by: 753
Author(s): David Otasek, John H. Morris, Jorge Bouças, Alexander Pico, Barry Demchak
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-67588-0

Glomerular endothelial cell heterogeneity in Alport syndrome
Cited 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