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: networkD3
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/networkD3
D3 JavaScript Network Graphs from R
14 versions
Latest release: over 7 years ago
31 dependent packages
16,327 downloads last month
Papers Mentioning networkD3 37
10.1016/j.scitotenv.2020.140792
ESPRES: A web application for interactive analysis of multiple pressures in aquatic ecosystemsCited by: 4
Author(s): Ángel Údias, Alberto Pistocchi, Olga Vigiak, Bruna Grizzetti, F. Bouraoui, César Alfaro
Software Mentions: 18
Published: about 4 years ago
10.3390/cells10082013
ChroMo, an Application for Unsupervised Analysis of Chromosome Movements in MeiosisCited by: 0
Author(s): Daniel León-Periñán, Alfonso Fernández-Álvarez
Software Mentions: 17
Published: over 3 years ago
10.1093/jas/skaa402
ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1Cited 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 dataCited 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
10.1186/s12967-021-02773-x
Multi-omics characterization and validation of invasiveness-related molecular features across multiple cancer typesCited by: 5
Author(s): Guoshu Bi, Jiaqi Liang, Yuansheng Zheng, Runmei Li, Mengnan Zhao, Yiwei Huang, Cheng Zhan, Songtao Xu, Hong Fan
Software Mentions: 15
Published: over 3 years ago
10.1186/s13073-021-00893-z
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelersCited by: 18
Author(s): Alaric W. D’Souza, Manish Boolchandani, Sanket Patel, Gianluca Galazzo, Jarne M. van Hattem, Maris S Arcilla, Damian C. Melles∗, Menno D. de Jong, Constance Schultsz, Gautam Dantas, John Penders
Software Mentions: 13
Published: over 3 years ago
10.1186/s12967-021-02889-0
Pan-cancer characterization of metabolism-related biomarkers identifies potential therapeutic targetsCited by: 6
Author(s): Guoshu Bi, Yunyi Bian, Jiaqi Liang, Jiacheng Yin, Runmei Li, Mengnan Zhao, Yiwei Huang, Tao Lu, Cheng Zhan, Hong Fan, Qun Wang
Software Mentions: 13
Published: over 3 years ago
10.12688/gatesopenres.12929.1
Towards an off-grid fecal sludge treatment unit: demonstrating energy positive thermal treatmentCited by: 1
Author(s): Taylor Myers, Lars Schoebitz, Stuart Woolley, Jaime Sanchez Ferragut, James O. Thostenson, Kathy Jooss, Jeffery Piascik, August Frechette, Nico Hotz, Brian R. Stoner, J.B. Hallowell
Software Mentions: 12
Published: over 5 years ago
10.3389/fgene.2019.01079
HiCeekR: A Novel Shiny App for Hi-C Data AnalysisCited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: about 5 years ago
10.1186/s12859-016-1260-x
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmapsCited by: 14
Author(s): Bohdan B. Khomtchouk, John L. Hennessy, Claes Wahlestedt
Software Mentions: 12
Published: about 8 years ago
10.1371/journal.pone.0216723
A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to MexicoCited by: 10
Author(s): Juliano Palacios‐Abrantes, Andrés M. Cisneros‐Montemayor, Miguel Á. Cisneros-Mata, Laura Rodríguez, Francisco Arreguı́n-Sánchez, Verónica Aguilar, Santiago Domínguez-Sánchez, Stuart Fulton, Raquel López-Sagástegui, Héctor Reyes‐Bonilla, Rocío Rivera-Campos, Silvia Salas, Nuno Simões, William W. L. Cheung
Software Mentions: 10
Published: over 5 years ago
10.1371/journal.pbio.2004045
A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebratesCited by: 41
Author(s): Jean-Louis Plouhinec, Sofía Medina-Ruíz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael B. Eisen, Richard M. Harland, Anne H. Monsoro-Burq
Software Mentions: 9
Published: about 7 years ago
10.1093/rheumatology/keab060
Do people with rheumatoid arthritis maintain their physical activity level at treatment onset over the first year of methotrexate therapy?Cited by: 4
Author(s): James M Gwinnutt, Husain Alsafar, Kimme L Hyrich, Mark Lunt, Anne Barton, Suzanne Verstappen, Rams co-investigators
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
10.3389/fonc.2020.622251
Screening and Identification of Four Prognostic Genes Related to Immune Infiltration and G-Protein Coupled Receptors Pathway in Lung AdenocarcinomaCited by: 3
Author(s): Yan Wang, Longqing Qiu, Yu Chen, Xia Zhang, Yang Peng, Feng Xu
Software Mentions: 7
Published: over 3 years ago
10.3390/nu13082610
Testing and Prescribing Vitamin B12 in Swiss General Practice: A Survey among PhysiciansCited by: 1
Author(s): Katarina Bardheci, Levy Jäger, L. Risch, Thomas Rosemann, Jakob M Burgstaller, Stefan Markun
Software Mentions: 6
Published: over 3 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
10.1371/journal.pone.0227258
Accelerated brain aging towards transcriptional inversion in a zebrafish model of the K115fs mutation of human PSEN2Cited by: 29
Author(s): Nhi Hin, Morgan Newman, Jan Kaslin, Alon M. Douek, Amanda L. Lumsden, Seyyed Hani Moussavi Nik, Yang Dong, Xin Zhou, Noralyn B. Mañucat-Tan, Alastair J. Ludington, David L. Adelson, Stephen Pederson, Michael Lardelli
Software Mentions: 6
Published: almost 5 years ago
10.3389/fmicb.2021.614957
Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type StrainsCited by: 34
Author(s): Camila Gazolla Volpiano, Fernando Hayashi Sant’Anna, Adriana Ambrosini, Jackson Freitas Brilhante de São José, Anelise Beneduzi, William B. Whitman, Emanuel Maltempi de Souza, Bruno Brito Lisboa, Luciano Kayser Vargas, Luciane Maria Pereira Passaglia
Software Mentions: 6
Published: over 3 years ago
10.7150/jca.55570
Upregulating <i>KTN1</i> promotes Hepatocellular Carcinoma progressionCited by: 1
Author(s): Jian Pan, Naixia Chao, Yao‐Yao Zhang, Tianyi Huang, Chengxiao Chen, Qiuhong Qin, Jinhong Guo, Rongshi Huang, Guopei Luo
Software Mentions: 6
Published: almost 4 years ago
10.1007/s00248-020-01657-9
Identifying Potential Hosts of Short-Branch MicrosporidiaCited by: 3
Author(s): Annemie Doliwa, Micah Dunthorn, Erika Rassoshanska, Frédéric Mahe, David Bass, Camila Duarte Ritter
Software Mentions: 5
Published: almost 4 years ago
10.1186/s12864-020-06915-1
Deciphering the mode of action and position of genetic variants impacting on egg number in broiler breedersCited by: 7
Author(s): Eirini Tarsani, Andreas Kranis, Gerasimos Maniatis, Santiago Avendaño, Ariadne L. Hager-Theodorides, A. Kominakis
Software Mentions: 5
Published: over 4 years ago
10.3390/ijms21030751
Effect of Bortezomib on Global Gene Expression in PC12-Derived Nerve CellsCited by: 10
Author(s): Karolina Łuczkowska, Dorota Rogińska, Zofia Ulańczyk, Bogusław Machaliński
Software Mentions: 5
Published: almost 5 years ago
10.1093/database/baz051
GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancerCited 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
10.1111/geb.13197
Simulating forest resilience: A reviewCited by: 41
Author(s): Katharina Albrich, Werner Rammer, Monica G. Turner, Zak Ratajczak, Kristin H. Braziunas, Winslow D. Hansen, Rupert Seidl
Software Mentions: 4
Published: about 4 years ago
10.3389/fgene.2020.00418
Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal CancerCited by: 12
Author(s): Li Guo, Guowei Yang, Yihao Kang, Sunjing Li, Rui Duan, Lulu Shen, Wenwen Jiang, Bowen Qian, Zibo Yin, Tingming Liang
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.ppat.1009439
A novel cell culture system modeling the SARS-CoV-2 life cycleCited by: 81
Author(s): Xiaohui Ju, Yangyong Zhu, Yuyan Wang, Jingrui Li, Jiaxing Zhang, Mingli Gong, Wenlin Ren, Sai Li, Jin Zhong, Linqi Zhang, Qiangfeng Cliff Zhang, Rong Zhang, Qiang Ding
Software Mentions: 3
Published: over 3 years ago
10.1007/s00335-019-09804-5
New models for human disease from the International Mouse Phenotyping ConsortiumCited by: 47
Author(s): Pilar Cacheiro, Melissa Haendel, Damian Smedley
Software Mentions: 3
Published: over 5 years ago
10.3389/fmicb.2021.683410
Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-ScaleCited by: 4
Author(s): Lauren Wind, Ishi Keenum, Suraj Gupta, Partha Pratim Ray, Katharine F. Knowlton, Monica A. Ponder, W. Cully Hession, Amy Pruden, Leigh‐Anne Krometis
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-020-64326-4
Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humansCited by: 7
Author(s): Pascal Gottmann, Meriem Ouni, Lisa Zellner, Markus Jähnert, Kilian Rittig, Dirk Walther, Annette Schürmann
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-019-45520-5
Discovery and characterization of functional modules associated with body weight in broilersCited by: 16
Author(s): Eirini Tarsani, Andreas Kranis, Gerasimos Maniatis, Santiago Avendaño, Ariadne L. Hager-Theodorides, A. Kominakis
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0243886
Adaptation and resilience of commercial fishers in the Northeast United States during the early stages of the COVID-19 pandemicCited by: 53
Author(s): Sarah Lindley Smith, Abigail S. Golden, Victoria C. Ramenzoni, Douglas R. Zemeckis, Olaf P. Jensen
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12934-020-01430-0
Gut microbial characteristics of adult patients with allergy rhinitisCited by: 31
Author(s): Lihong Zhu, Feng Xu, Wenrong Wan, Bin Yu, Lin Tang, Yiming Yang, Yali Du, Zhangran Chen, Hongxiang Xu
Software Mentions: 2
Published: about 4 years ago
10.3390/ijms21010350
Molecular Mechanisms of Bortezomib Action: Novel Evidence for the miRNA–mRNA Interaction InvolvementCited by: 18
Author(s): Karolina Łuczkowska, Dorota Rogińska, Zofia Ulańczyk, Edyta Paczkowska, Christian A. Schmidt, Bogusław Machaliński
Software Mentions: 2
Published: almost 5 years ago
10.3389/fmicb.2020.00576
Integrated Transcriptomic and Proteomic Analyses of the Interaction Between Chicken Synovial Fibroblasts and Mycoplasma synoviaeCited by: 5
Author(s): Rui Li, Bin Xu, Shuang Yu, Jingfeng Zhang, Huawei Sun, Chuanmin Liu, Fengying Lu, Qunxing Pan, Xiaofei Zhang
Software Mentions: 2
Published: over 4 years ago
10.1186/s12889-020-09873-1
Management of uncomplicated malaria among children under five years at public and private sector facilities in MaliCited by: 3
Author(s): Seydou Fomba, Daouda Koné, Bakary Doumbia, Diadier Diallo, Thomas Druetz, Lia Florey, Thomas P. Eisele, Erin Eckert, Jules Mihigo, Ruth A. Ashton
Software Mentions: 1
Published: almost 4 years ago
10.3390/ijms22179209
miRNAs as Regulators of the Early Local Response to Burn InjuriesCited by: 5
Author(s): Ines Foessl, Christoph Haudum, Ivan Vidakovic, Peter Ruth, Joakim Franz, Selma Mautner, Sonja Kainz, Elisabeth Hofmann, Barbara Obermayer‐Pietsch, Thomas Birngruber, Petra Kotzbeck
Software Mentions: 1
Published: about 3 years ago