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: cran: ggraph
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/ggraph
An Implementation of Grammar of Graphics for Graphs and Networks
11 versions
Latest release: about 2 years ago
99 dependent packages
47,271 downloads last month
Papers Mentioning ggraph 58
10.3389/fonc.2020.617890
Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal AdenocarcinomaCited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: almost 4 years ago
10.1007/s10734-020-00674-4
Lights, camera, active! appreciation of active learning predicts positive attitudes towards lecture captureCited by: 6
Author(s): Emily Nordmann, Anne L. Clark, Elliott Spaeth, Jill R D MacKay
Software Mentions: 18
Published: almost 4 years ago
10.1016/j.cell.2020.12.016
Spatiotemporal analysis of human intestinal development at single-cell resolutionCited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: almost 4 years ago
10.1186/s40168-019-0725-3
Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and hostCited by: 43
Author(s): Aonghus Lavelle, Thomas Hoffmann, Hang-Phuong Pham, Philippe Langella, Éric Guédon, Harry Sokol
Software Mentions: 16
Published: over 5 years ago
10.1371/journal.pone.0244876
Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomesCited by: 12
Author(s): Moamen M. Elmassry, Sunghwan Kim, Ben Busby
Software Mentions: 16
Published: almost 4 years ago
10.3390/biom10081095
Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo SimulationsCited by: 26
Author(s): Joel Markgren, Mikael S. Hedenqvist, Faiza Rasheed, Marie Skepö, Eva Johansson
Software Mentions: 15
Published: over 4 years ago
10.3390/biomedicines9020144
Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal TransfaunationCited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago
10.3390/biom10121606
A Customizable Analysis Flow in Integrative Multi-OmicsCited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago
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: over 3 years ago
10.1186/s13059-019-1783-3
AlleleAnalyzer: a tool for personalized and allele-specific sgRNA designCited by: 20
Author(s): Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard
Software Mentions: 14
Published: over 5 years ago
10.3389/fpubh.2020.00425
Political Consequences of COVID-19 and Media Framing in South KoreaCited by: 13
Author(s): Wonkwang Jo, Daesung Chang
Software Mentions: 12
Published: about 4 years ago
10.3389/fmed.2021.644724
Exploring the Clinical Characteristics of COVID-19 Clusters Identified Using Factor Analysis of Mixed Data-Based Cluster AnalysisCited by: 10
Author(s): Han Liang, Pan Shen, Jiahui Yan, Yao Huang, Xin Ba, Wei Chen Lin, Hui Wang, Ying Huang, Kai Qin, Yu Wei, Zhe Chen, Shenghao Tu
Software Mentions: 12
Published: over 3 years ago
10.3390/jcm10184071
Diagnostic and Prognostic Potential of MiR-379/656 MicroRNA Cluster in Molecular Subtypes of Breast CancerCited by: 2
Author(s): Megha Lal, Asgar Hussain Ansari, Anurag Agrawal, Arijit Mukhopadhyay
Software Mentions: 12
Published: about 3 years ago
10.3390/genes9120569
NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs TechnologiesCited by: 13
Author(s): Eduardo Zúñiga-León, Ulises Carrasco-Navarro, Francisco Fierro
Software Mentions: 12
Published: almost 6 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 CaribbeanCited 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
10.7717/peerj.4152
Population structure and phenotypic variation of<i>Sclerotinia sclerotiorum</i>from dry bean (<i>Phaseolus vulgaris</i>) in the United StatesCited by: 28
Author(s): Zhian N. Kamvar, Bimal S. Amaradasa, Rachana Jhala, Serena McCoy, James R. Steadman, Sydney E. Everhart
Software Mentions: 11
Published: almost 7 years ago
10.7150/thno.53092
Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapyCited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: almost 4 years ago
10.1093/gigascience/giy083
Clustering trees: a visualization for evaluating clusterings at multiple resolutionsCited by: 353
Author(s): Luke Zappia, Alicia Oshlack
Software Mentions: 9
Published: over 6 years ago
10.7717/peerj.11916
The composition, geography, biology and assembly of the coastal flora of the Cape Floristic RegionCited by: 5
Author(s): B. Adriaan Grobler, Richard M. Cowling
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0208370
Measuring popularity of ecological topics in a temporal dynamical knowledge networkCited by: 3
Author(s): Tian-Yuan Huang, Bin Zhao
Software Mentions: 8
Published: almost 6 years ago
10.1038/s41598-021-87837-0
A social network analysis of the spread of COVID-19 in South Korea and policy implicationsCited by: 34
Author(s): Wonkwang Jo, Daesung Chang, Myoungsoon You, Ghi Hoon Ghim
Software Mentions: 8
Published: over 3 years ago
10.3390/biom11050695
Variations in Gut Microbiome are Associated with Prognosis of Hypertriglyceridemia-Associated Acute PancreatitisCited by: 10
Author(s): Xiaomin Hu, Liang Gong, Ronggang Zhou, Ziying Han, Ji Li, Yan Zhang, Shuyang Zhang, Dong Wu
Software Mentions: 8
Published: over 3 years ago
10.1099/mgen.0.000244
Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host rangesCited by: 10
Author(s): Lauren Brooks, Mo Kaze, Mark Sistrom
Software Mentions: 7
Published: almost 6 years ago
10.7717/peerj.4718
<i>phylopath</i>: Easy phylogenetic path analysis in RCited by: 90
Author(s): Wouter van der Bijl
Software Mentions: 7
Published: over 6 years ago
10.1186/s12864-021-07441-4
A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networksCited by: 2
Author(s): Pedro Gabriel Nachtigall, Luiz Augusto Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Software Mentions: 7
Published: over 3 years ago
10.3389/fimmu.2020.596514
Intestinal Transcriptome Analysis Reveals Soy Derivative-Linked Changes in Atlantic SalmonCited by: 26
Author(s): Viswanath Kiron, Youngjin Park, Prabhugouda Siriyappagouder, Dalia Dahle, Ghana Kalerammana Vasanth, Jorge Dias, Jorge M. O. Fernandes, Mette Sørensen, Viviane Verlhac Trichet
Software Mentions: 7
Published: almost 4 years ago
10.3389/fpls.2019.01521
The Contribution of Functional Traits to the Breeding Progress of Central-European Winter Wheat Under Differing Crop Management IntensitiesCited by: 14
Author(s): Till Rose, Henning Kage
Software Mentions: 7
Published: almost 5 years ago
10.1038/s41598-021-88745-z
A Graph Theory approach to assess nature’s contribution to people at a global scaleCited by: 13
Author(s): Sílvia de Juan, Andrés Ospina-Álvarez, Sebastián Villasante, Ana Ruiz‐Frau
Software Mentions: 7
Published: over 3 years ago
10.18632/aging.103168
Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosisCited by: 103
Author(s): Jianquan He, Shuaimei Xu, Bangzhou Zhang, Chuanxing Xiao, Zhangran Chen, Fuyou Si, Jifan Fu, Xiaobo Lin, Guohua Zheng, Guangchuang Yu, Jian Chen
Software Mentions: 6
Published: over 4 years ago
10.1186/s12859-020-03818-6
Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humansCited by: 2
Author(s): Meng Li
Software Mentions: 6
Published: about 4 years ago
10.3390/metabo11040194
Plasma Metabolomic Profiling in 1391 Subjects with Overweight and Obesity from the SPHERE StudyCited by: 12
Author(s): G. Frigerio, Chiara Favero, Diego Savino, Rosa Mercadante, Benedetta Albetti, Laura Dioni, Luisella Vigna, Valentina Bollati, Angela Cecilia Pesatori, Silvia Fustinoni
Software Mentions: 6
Published: over 3 years ago
10.3390/microorganisms8091367
Lifestyle, Lineage, and Geographical Origin Influence Temperature-Dependent Phenotypic Variation across Yeast Strains during Wine FermentationCited by: 4
Author(s): Rebecca C. Deed, Lisa I. Pilkington
Software Mentions: 6
Published: about 4 years ago
10.1007/s00421-021-04676-7
Individual cardiovascular responsiveness to work-matched exercise within the moderate- and severe-intensity domainsCited by: 17
Author(s): Felipe Mattioni Maturana, Philipp Schellhorn, Gunnar Erz, Christof Burgstahler, Manuel Widmann, Barbara Munz, Rogério N. Soares, Juan M. Murias, Ansgar Thiel, Andreas M. Nieß
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-018-37512-8
Sheathless CE-MS based metabolic profiling of kidney tissue section samples from a mouse model of Polycystic Kidney DiseaseCited by: 22
Author(s): Elena Sánchez-López, Guinevere S. M. Kammeijer, Antonio L. Crego, Marı́a Luisa Marina, Rawi Ramautar, Dorien J.M. Peters, Oleg A. Mayboroda
Software Mentions: 6
Published: almost 6 years ago
10.1038/s41598-021-86032-5
A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytesCited by: 18
Author(s): Timothy Warwick, Marcel H. Schulz, Stefan Günther, Ralf Gilsbach, Antonio Neme, Carsten Carlberg, Ralf P. Brandes, Sabine Seuter
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-021-97805-3
Differences and similarities in the conceptualization of COVID-19 and other diseases in the first Italian lockdownCited by: 6
Author(s): Claudia María, Ilenia Falcinelli, Arthur-Henri Michalland, Luca Tummolini, Anna M. Borghi
Software Mentions: 6
Published: about 3 years ago
10.1371/journal.pone.0242955
Lessons from movement ecology for the return to work: Modeling contacts and the spread of COVID-19Cited by: 4
Author(s): Allison K. Shaw, Lauren A. White, Matthew Michalska‐Smith, Elizabeth T. Borer, Meggan E. Craft, Eric W. Seabloom, Emilie C. Snell‐Rood, Michael Travisano
Software Mentions: 5
Published: almost 4 years ago
10.3389/fgene.2021.706854
Crosslink: An R Package for Network Visualization of Grouped NodesCited by: 1
Author(s): Di Liu, Zhijie Bai, Bing Liu, Zongcheng Li
Software Mentions: 5
Published: over 3 years ago
10.3390/ani11051229
A Preliminary Investigation of Social Network Analysis Applied to Dairy Cow Behavior in Automatic Milking System EnvironmentsCited by: 2
Author(s): Liliana Fadul-Pacheco, Michael Liou, Douglas J. Reinemann, Víctor E. Cabrera
Software Mentions: 5
Published: over 3 years ago
10.1093/hmg/ddaa140
Motor neuron translatome reveals deregulation of SYNGR4 and PLEKHB1 in mutant TDP-43 amyotrophic lateral sclerosis modelsCited by: 13
Author(s): Rita F Marques, Jan Broder Engler, Katrin Küchler, Ross A. Jones, Thomas Lingner, Gabriela Salinas, Thomas H. Gillingwater, Manuel A. Friese, Kent E. Duncan
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2020.00680
Identification of a Six-Immune-Related Long Non-coding RNA Signature for Predicting Survival and Immune Infiltrating Status in Breast CancerCited by: 24
Author(s): Zheng Li, Yaming Li, Xiaolong Wang
Software Mentions: 5
Published: over 4 years ago
10.1186/s40168-021-01018-9
Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndromeCited by: 24
Author(s): Julien Tap, Stine Störsrud, Boris Le Nevé, Aurélie Cotillard, Nicolas Pons, Joël Doré, Lena Öhman, Hans Törnblom, Muriel Derrien, Magnus Simrén
Software Mentions: 5
Published: over 3 years ago
10.3389/fmolb.2020.605623
Long Non-coding RNA BTG3-7:1 and JUND Co-regulate C21ORF91 to Promote Triple-Negative Breast Cancer ProgressCited by: 0
Author(s): Dan Zheng, Xiujing He, Ting Luo, Xiaorong Zhong, Hong Zheng, Jiqiao Yang, Yanchu Li, Jing Jing
Software Mentions: 4
Published: almost 4 years ago
10.1099/mgen.0.000569
Genomic and temporal analyses of Mycobacterium bovis in southern BrazilCited by: 7
Author(s): Rudielle de Arruda Rodrigues, Flábio R. Araújo, Alberto M. R. Dávila, Rodrigo Nestor Etges, Julian Parkhill, Andries J. van Tonder
Software Mentions: 4
Published: over 3 years ago
10.1186/s12874-021-01352-4
Symptom clusters among cancer survivors: what can machine learning techniques tell us?Cited by: 6
Author(s): Koen Ilja Neijenhuijs, Carel F.W. Peeters, Henk van Weert, Pim Cuijpers, I. Verdonck-de Leeuw
Software Mentions: 4
Published: over 3 years ago
10.1038/s41438-021-00502-5
Strawberry sweetness and consumer preference are enhanced by specific volatile compoundsCited by: 41
Author(s): Zhen Fan, Tomas Hasing, Timothy S. Johnson, Drake M. Garner, Michael L. Schwieterman, Christopher R. Barbey, Thomas A. Colquhoun, Charles A. Sims, M. D. V. de Resende, Vance M. Whitaker
Software Mentions: 4
Published: over 3 years ago
10.3389/fpsyt.2021.628397
Facial and Vocal Expressions During Clinical Interviews Suggest an Emotional Modulation Paradox in Borderline Personality Disorder: An Explorative StudyCited by: 1
Author(s): Javier Villanueva-Valle, José-Luis Dı́az, Said Jiménez, Andrés Rodríguez-Delgado, Iván Arango de Montis, Areli León-Bernal, Edgar Miranda-Terrés, Jairo Muñóz-Delgado
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0232512
Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban BathsCited by: 5
Author(s): Antonino De Natale, Bruno Hay Mele, Paola Cennamo, Angelo Del Mondo, Mariagioia Petraretti, Antonino Pollio
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pgen.1006817
Pervasive antagonistic interactions among hybrid incompatibility lociCited by: 45
Author(s): Rafael F. Guerrero, Christopher D. Muir, Sarah Josway, Leonie C. Moyle
Software Mentions: 3
Published: over 7 years ago
10.1126/sciadv.abd7225
Global political responsibility for the conservation of albatrosses and large petrelsCited by: 32
Author(s): Martin Beal, Maria P. Dias, Richard A. Phillips, Steffen Oppel, Carolina Hazin, Elizabeth J. Pearmain, Josh Adams, David J. Anderson, Michelle Antolos, Javier Arata, José Manuel Arcos, John P. Y. Arnould, Jill A. Awkerman, Elizabeth A. Bell, Mike Bell, Mark J. Carey, Ryan D. Carle, Thomas A. Clay, Jaimie Cleeland, Valentina Colodro, Melinda G. Conners, Marta Cruz‐Flores, Richard Cuthbert, Karine Delord, Lorna Deppe, Ben J. Dilley, Herculano Dinis, Graeme Elliott, Fernanda De Felipe, Jonathan J. Felis, Manuela G. Forero, Amanda N. D. Freeman, Akira Fukuda, Jacob González‐Solís, José Pedro Granadeiro, April Hedd, Peter Hodum, José Manuel Igual, A. Jaeger, Todd J. Landers, Matthieu Le Corre, Azwianewi B. Makhado, Benjamin Metzger, Teresa Militão, William A. Montevecchi, Virginia Morera‐Pujol, Leia Navarro-Herrero, Deon Nel, David G. Nicholls, Daniel Oró, Ridha Ouni, Kiyoaki Ozaki, Flavio Quintana, Raül Ramos, Tim Reid, José Manuel Reyes‐González, Christopher T. Robertson, Graham Robertson, Mohamed Salah Romdhane, Peter G. Ryan, Paul M. Sagar, Fumio Sato, Stefan Schoombie, R. Paul Scofield, Scott A. Shaffer, Nirmal Shah, Kim L. Stevens, C. Surman, Robert M. Suryan, Akinori Takahashi, Vikash Tatayah, Graeme A. Taylor, David R. Thompson, Leigh G. Torres, Kath Walker, Ross M. Wanless, Susan M. Waugh, Henri Weimerskirch, Takashi Yamamoto, Zuzana Zajková, Laura Zango, Paulo Catry
Software Mentions: 3
Published: over 3 years ago
10.1128/mSphere.00239-19
Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and ResistomesCited by: 30
Author(s): Giselle Kristi Guron, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden, Monica A. Ponder
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-021-89126-2
HNF1A regulates colorectal cancer progression and drug resistance as a downstream of POU5F1Cited by: 7
Author(s): Shiki Fujino, Norikatsu Miyoshi, Aya Ito, Masayoshi Yasui, Chu Matsuda, Masayuki Ohue, Mamoru Uemura, Tsunekazu Mizushima, Yuichiro Doki, Hidetoshi Eguchi
Software Mentions: 3
Published: over 3 years ago
10.3389/fpls.2017.01524
Identification of Biomarkers for Defense Response to Plasmopara viticola in a Resistant Grape VarietyCited by: 53
Author(s): Giulia Chitarrini, Evelyn Soini, Samantha Riccadonna, Pietro Franceschi, L. Zulini, Domenico Masuero, A. Vecchione, M. Stefanini, Gabriele Di Gaspero, Fulvio Mattivi, Urška Vrhovšek
Software Mentions: 2
Published: about 7 years ago
10.1186/s13223-021-00569-8
Pre-existing asthma as a comorbidity does not modify cytokine responses and severity of COVID-19Cited by: 2
Author(s): Jian Luo, Yi‐Ling Chen, Wentao Chen, David A. Duncan, Alexander J. Mentzer, Julian C. Knight, Graham S. Ogg, Paul Klenerman, Ian Pavord, Luzheng Xue
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms221810144
Differential Regulation of Interferon Signaling Pathways in CD4+ T Cells of the Low Type-2 Obesity-Associated Asthma PhenotypeCited by: 10
Author(s): Fahd Alhamdan, Leigh M. Marsh, Frauke Pedersen, Bilal Alashkar Alhamwe, Clemens Thölken, Petra Ina Pfefferle, Thomas Bahmer, Timm Greulich, Daniel P. Potaczek, Holger Garn
Software Mentions: 1
Published: about 3 years ago
10.1007/s00508-020-01723-9
Emergence of coronavirus disease 2019 (COVID-19) in AustriaCited by: 46
Author(s): Peter Kreidl, Daniela Schmid, Sabine Maritschnik, Lukas Richter, Wegene Borena, Jakob-Wendelin Genger, Alexandra Popa, Thomas Penz, Christoph Bock, Andréas Bergthaler, Franz Allerberger
Software Mentions: 1
Published: over 4 years ago
10.3389/fpsyg.2021.682838
The Building Blocks of Child Bilingual Code-Mixing: A Cross-Corpus Traceback ApproachCited by: 6
Author(s): Antje Endesfelder Quick, Stefan Hartmann
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-020-69051-6
Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevineCited by: 22
Author(s): Giulia Chitarrini, Samantha Riccadonna, L. Zulini, A. Vecchione, M. Stefanini, Simone Larger, Massimo Pindo, Alessandro Cestaro, Pietro Franceschi, Gabriele Magris, Serena Foria, Michèle Morgante, Gabriele Di Gaspero, Urška Vrhovšek
Software Mentions: 1
Published: over 4 years ago