cran: visNetwork | Projects | Ecosyste.ms: Papers

10.1186/s12859-017-1905-4

ADAGE signature analysis: differential expression analysis with data-defined gene sets
Cited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: almost 7 years ago

10.1038/s41598-020-78469-x

Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
Cited by: 14
Author(s): Jacob Cardenas, Uthra Balaji, Jin Gu
Software Mentions: 23
Published: almost 4 years ago

10.1186/s13321-020-00477-w

patRoon: open source software platform for environmental mass spectrometry based non-target screening
Cited by: 76
Author(s): Rick Helmus, Thomas L. ter Laak, Annemarie P. van Wezel, P. de Voogt, Emma L. Schymanski
Software Mentions: 20
Published: almost 4 years ago

10.1186/s12859-018-2351-7

wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool
Cited by: 36
Author(s): Deisy Morselli Gysi, André Voigt, Tiago de Miranda Fragoso, Eivind Almaas, Katja Nowick
Software Mentions: 17
Published: about 6 years ago

10.1093/gigascience/giz061

LION/web: a web-based ontology enrichment tool for lipidomic data analysis
Cited by: 110
Author(s): Martijn R. Molenaar, Aike Jeucken, Tsjerk A. Wassenaar, Chris H.A. van de Lest, Jos F. Brouwers, J. Bernd Helms
Software Mentions: 16
Published: over 5 years ago

10.1093/jas/skaa402

ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1
Cited by: 4
Author(s): Gota Morota, Hao Cheng, Dianne Cook, Emi Tanaka
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-017-1994-0

PIVOT: platform for interactive analysis and visualization of transcriptomics data
Cited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Software Mentions: 15
Published: almost 7 years ago

10.3389/fgene.2021.652189

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: over 3 years ago

10.7554/eLife.57116

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
Cited by: 35
Author(s): Kenichi Shimada, John A. Bachman, Jeremy Muhlich, Timothy J. Mitchison
Software Mentions: 13
Published: almost 4 years ago

10.3389/fpubh.2021.649190

Shifting From Sectoral to Integrated Surveillance by Changing Collaborative Practices: Application to West Nile Virus Surveillance in a Small Island State of the Caribbean
Cited by: 2
Author(s): Mariana Geffroy, Nonito Pagès, David Chavernac, Alexis Dereeper, L. Aubert, Cécile Herrmann-Storck, Anubis Vega-Rúa, Sylvie Lecollinet, Jennifer Pradel
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: almost 5 years ago

10.12688/f1000research.13925.3

BED: a Biological Entity Dictionary based on a graph data model
Cited by: 1
Author(s): Patrice Godard, Jonathan van Eyll
Software Mentions: 10
Published: over 6 years ago

10.7717/peerj.10264

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
Cited by: 6
Author(s): Elly Poretsky, Alisa Huffaker
Software Mentions: 10
Published: about 4 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pcbi.1008918

Genome-wide analysis of lncRNA stability in human
Cited by: 17
Author(s): Kaiwen Shi, Tao Liu, Hanjiang Fu, Wuju Li, Xiaofei Zheng
Software Mentions: 9
Published: over 3 years ago

10.1186/s12943-021-01405-8

Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality
Cited by: 6
Author(s): Salvatore Benfatto, Özdemirhan Serçin, Francesca R. Dejure, Amir Abdollahi, Frank T. Zenke, Balca R. Mardin
Software Mentions: 9
Published: about 3 years ago

10.1186/s12859-019-3105-x

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
Cited by: 190
Author(s): Valerio Licursi, Federica Conte, Giulia Fiscon, Paola Paci
Software Mentions: 8
Published: about 5 years ago

10.1099/mgen.0.000244

Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges
Cited by: 10
Author(s): Lauren Brooks, Mo Kaze, Mark Sistrom
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12859-021-04012-y

CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network
Cited by: 4
Author(s): Wen Xiao, Lin Gao, Tuo Song, Chaoqun Jiang
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pcbi.1009302

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge
Cited by: 5
Author(s): Zhitao Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug Dream Challenge Community, Kristen K. Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan
Software Mentions: 7
Published: about 3 years ago

10.12688/f1000research.16032.3

epiflows: an R package for risk assessment of travel-related spread of disease
Cited by: 3
Author(s): Paula Moraga, Ilaria Dorigatti, Zhian N. Kamvar, Paweł Piątkowski, Salla Toikkanen, VP Nagraj, Christl A. Donnelly, Thibaut Jombart
Software Mentions: 7
Published: about 5 years ago

10.12688/f1000research.19410.1

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem
Cited by: 0
Author(s): Shian Su, Vincent J. Carey, Lori Shepherd, Matthew E. Ritchie, Martin Morgan, Sean Davis
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-020-73083-3

Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs
Cited by: 12
Author(s): Hiu Wai Lee, Borja Esteve‐Altava, Arhat Abzhanov
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1005694

PCSF: An R-package for network-based interpretation of high-throughput data
Cited by: 34
Author(s): Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
Software Mentions: 6
Published: over 7 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

10.1186/s12859-019-3309-0

shinyBN: an online application for interactive Bayesian network inference and visualization
Cited by: 10
Author(s): Jia-Jin Jason Chen, Ruyang Zhang, Xuesi Dong, Lijuan Lin, Ying Zhu, Jieyu He, David C. Christiani, Yongyue Wei, Feng Chen
Software Mentions: 6
Published: almost 5 years ago

10.3389/fvets.2020.00189

Network Analysis of Swine Shipments in China: The First Step to Inform Disease Surveillance and Risk Mitigation Strategies
Cited by: 8
Author(s): Kathleen C. O'Hara, Rui Zhang, Yong Sam Jung, Xiaobing Zhou, Yingjuan Qian, Beatriz Martínez‐López
Software Mentions: 5
Published: over 4 years ago

10.1093/bioinformatics/btaa662

<i>treeheatr</i>: an R package for interpretable decision tree visualizations
Cited by: 13
Author(s): Trang T. Le, Jason H. Moore
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008098

A machine learning and network framework to discover new indications for small molecules
Cited by: 8
Author(s): Coryandar Gilvary, Jamal Elkhader, Neel S. Madhukar, Claire Henchcliffe, Marcus D. Goncalves, Olivier Elemento
Software Mentions: 5
Published: over 4 years ago

10.1186/s13073-017-0492-3

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
Cited by: 63
Author(s): Xun Zhu, Thomas Wolfgruber, Austin Tasato, Cédric Arisdakessian, David Garmire, Lana X. Garmire
Software Mentions: 5
Published: almost 7 years ago

10.3390/biology10070665

FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists
Cited by: 22
Author(s): Foteini Thanati, Evangelos Karatzas, Fotis A. Baltoumas, Dimitrios J. Stravopodis, Aristides G. Eliopoulos, Georgios A. Pavlopoulos
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.9395

Doing nothing and what it looks like: inactivity in fattening cattle
Cited by: 8
Author(s): Sara Hintze, Freija Maulbetsch, Lucy Asher, Christoph Winckler
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-017-4242-0

Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria
Cited by: 16
Author(s): Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Manuel Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2021.620002

AMRmap: An Interactive Web Platform for Analysis of Antimicrobial Resistance Surveillance Data in Russia
Cited by: 24
Author(s): Alexey Yu. Kuzmenkov, Ivan V. Trushin, Alina G. Vinogradova, Andrey A. Avramenko, М В Сухорукова, Surbhi Malhotra-Kumar, А В Дехнич, Mikhail V. Edelstein, Roman Kozlov
Software Mentions: 4
Published: over 3 years ago

10.1093/database/baz051

GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer
Cited by: 3
Author(s): Ying Wang, Yueqian Wang, Shuangkuai Wang, Yuantao Tong, Ling Jin, Hui Zong, Rongbin Zheng, Jiancheng Yang, Zeyu Zhang, En Ouyang, Min Zhou, Xiaoyan Zhang
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.101751

miRNA-mRNA crosstalk in myocardial ischemia induced by calcified aortic valve stenosis
Cited by: 12
Author(s): Chenyang Duan, Zhijun Cao, Fuqin Tang, Jian Zhao, Chunshui Liang, Hong Liu, Xiao Ye, Liangming Liu, Rong Ma
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0196588

FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer
Cited by: 42
Author(s): Priyabrata Panigrahi, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: over 6 years ago

10.1093/database/baab048

LINPS: a database for cancer-cell-specific perturbations of biological networks
Cited by: 1
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms21093171

DRUGPATH: The Drug Gene Pathway Meta-Database
Cited by: 3
Author(s): Rajeev Jaundoo, Travis J. A. Craddock
Software Mentions: 3
Published: over 4 years ago

10.12688/f1000research.14492.2

epicontacts: Handling, visualisation and analysis of epidemiological contacts
Cited by: 12
Author(s): VP Nagraj, Nistara Randhawa, Finlay Campbell, Thomas Crellen, Bertrand Súdre, Thibaut Jombart
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-019-5548-x

iGEAK: an interactive gene expression analysis kit for seamless workflow using the R/shiny platform
Cited by: 35
Author(s): Kwangmin Choi, Nancy Ratner
Software Mentions: 3
Published: over 5 years ago

10.1186/s13007-018-0345-0

DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R
Cited by: 4
Author(s): Maja Zagorščak, Andrej Blejec, Živa Ramšak, Marko Petek, Tjaša Stare, Kristina Gruden
Software Mentions: 2
Published: about 6 years ago

10.3389/fmed.2021.662460

Pan-Cancer Analysis of Genomic and Prognostic Characteristics Associated With Coronavirus Disease 2019 Regulators
Cited by: 6
Author(s): Jian Zhang, Huali Jiang, Kunpeng Du, Tao Xie, Baiyao Wang, Chengcong Chen, Bohong Cen, Yawei Yuan, Jiacai Ye
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-11786-w

Digging into the low molecular weight peptidome with the OligoNet web server
Cited by: 11
Author(s): Youzhong Liu, Sara Forcisi, Marianna Lucio, Mourad Harir, Florian Bahut, Magali Déléris-Bou, Sibylle Krieger-Weber, Régis D. Gougeon, Hervé Alexandre, Philippe Schmitt‐Kopplin
Software Mentions: 1
Published: about 7 years ago

10.4178/epih.e2021018

Comorbidity network analysis related to obesity in middle-aged and older adults: findings from Korean population-based survey data
Cited by: 12
Author(s): Hye Ah Lee, Hyesook Park
Software Mentions: 1
Published: over 3 years ago

10.3390/jof7070545

Risk Factors for Fungal Co-Infections in Critically Ill COVID-19 Patients, with a Focus on Immunosuppressants
Cited by: 33
Author(s): Obinna T. Ezeokoli, Onele Gcilitshana, Carolina H. Pohl
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-019-40826-w

Six novel immunoglobulin genes as biomarkers for better prognosis in triple-negative breast cancer by gene co-expression network analysis
Cited by: 29
Author(s): Huan Ming Hsu, Chi Ming Chu, Yu Jia Chang, Jyh Cherng Yu, Chien-Ting Chen, Chen En Jian, Chia-Yi Lee, Yueh Tao Chiang, Ching-Wei Chang, Yu Sheng Chang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0204016

WEADE: A workflow for enrichment analysis and data exploration
Cited by: 3
Author(s): Nils Trost, Eugen Rempel, Olga Ermakova, Srividya Tamirisa, Letiția Pârcălăbescu, Michael Boutros, Jan U. Lohmann, Ingrid Lohmann
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-50403-w

Risk of African swine fever virus introduction into the United States through smuggling of pork in air passenger luggage
Cited by: 38
Author(s): Cristina Jurado, Lina Mur, María Sol Pérez Aguirreburualde, Estefanía Cadenas-Fernández, Beatriz Martínez‐López, José Manuel Sánchez‐Vizcaíno, Andrés Perez
Software Mentions: 1
Published: about 5 years ago

Projects: cran: visNetwork

Papers Mentioning visNetwork 49