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: RedeR
https://packages.ecosyste.ms/registries/bioconductor.org/packages/RedeR
Interactive visualization and manipulation of nested networks
1 version
Latest release: 10 months ago
4 dependent packages
44,230 downloads total
Papers Mentioning RedeR 21
10.3390/metabo9100200
The metaRbolomics Toolbox in Bioconductor and beyondCited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: almost 5 years ago
10.3390/biology3010085
R-Based Software for the Integration of Pathway Data into Bioinformatic AlgorithmsCited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: over 10 years ago
10.1002/cam4.2493
Integrated transcriptomics reveals master regulators of lung adenocarcinoma and novel repositioning of drug candidatesCited by: 12
Author(s): Marco Antônio De Bastiani, Fábio Klamt
Software Mentions: 8
Published: almost 5 years ago
10.1186/s40478-017-0421-0
Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body miceCited by: 5
Author(s): Anita Lakatos, Natalie R.S. Goldberg, Mathew Blurton‐Jones
Software Mentions: 8
Published: over 7 years ago
10.3389/fendo.2021.672319
Adrenocortical Carcinoma Steroid Profiles: In Silico Pan-Cancer Analysis of TCGA Data Uncovers Immunotherapy Targets for Potential Improved OutcomesCited by: 6
Author(s): João C. D. Muzzi, Jessica Maria Magno, Milena A. Cardoso, Juliana de Moura, Mauro A. A. Castro, Bonald C. Figueiredo
Software Mentions: 7
Published: about 3 years ago
10.1186/gb-2012-13-4-r29
RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.Cited by: 84
Author(s): Mauro A. A. Castro, Xin Wang, Michael Fletcher, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 7
Published: over 12 years ago
10.1186/s13059-015-0675-4
Extensive rewiring of epithelial-stromal co-expression networks in breast cancerCited by: 42
Author(s): Eunsun Oh, Stephen M Christensen, Sindhu Ghanta, Jong Cheol Jeong, Octavian Bucur, Benjamin Glass, Laleh Montaser‐Kouhsari, Nicholas W. Knoblauch, Nicholas Bertos, Sadiq M.I. Saleh, Benjamin Haibe‐Kains, Morag Park, Andrew H. Beck
Software Mentions: 7
Published: about 9 years ago
10.3389/fnins.2012.00187
Systems Biology, Bioinformatics, and Biomarkers in NeuropsychiatryCited by: 43
Author(s): Ali Alawieh, Fadi A. Zaraket, Jianliang Li, Stefania Mondello, Amaly Nokkari, Mahdi Razafsha, Bilal H. Fadlallah, Rose‐Mary Boustany, Firas Kobeissy
Software Mentions: 7
Published: over 12 years ago
10.1186/s13195-018-0394-7
Alzheimer’s disease master regulators analysis: search for potential molecular targets and drug repositioning candidatesCited by: 62
Author(s): Daiani Machado de Vargas, Marco Antônio De Bastiani, Eduardo R. Zimmer, Fábio Klamt
Software Mentions: 4
Published: about 6 years ago
10.1038/srep29832
Identification of host transcriptional networks showing concentration-dependent regulation by HPV16 E6 and E7 proteins in basal cervical squamous epithelial cellsCited by: 7
Author(s): Stephen Smith, Cinzia G. Scarpini, Ian J. Groves, Richard Odle, Nicholas Coleman
Software Mentions: 4
Published: about 8 years ago
10.18632/aging.102579
Discovering master regulators in hepatocellular carcinoma: one novel MR, SEC14L2 inhibits cancer cellsCited by: 14
Author(s): Zhihui Li, Yi Liu, Guoyan Tian, Jianyue Wu, Anqian Lu, Jin Chen, Beibei Xu, Junping Shi, Jin Yang
Software Mentions: 4
Published: over 4 years ago
10.1186/s12885-015-1179-z
Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinomaCited by: 57
Author(s): Yibin Hao, Wei Wu, Fachun Shi, Rodrigo Juliani Siqueira Dalmolin, Ming Yan, Fei Tian, Xiaobing Chen, Guoyong Chen, Wei Cao
Software Mentions: 4
Published: over 9 years ago
10.1038/s41598-019-52299-y
Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in PlantsCited by: 15
Author(s): Raffael Azevedo de Carvalho Oliveira, Abraão Silveira de Andrade, Danilo Oliveira Imparato, Juliana Gabriela Silva de Lima, Ricardo Victor Machado de Almeida, Jorge Lima, Matheus Augusto de Bittencourt Pasquali, Rodrigo Juliani Siqueira Dalmolin
Software Mentions: 3
Published: over 4 years ago
10.1523/JNEUROSCI.2905-20.2021
Differential Expression Levels of Sox9 in Early Neocortical Radial Glial Cells Regulate the Decision between Stem Cell Maintenance and DifferentiationCited by: 10
Author(s): Jaime Fabra-Beser, Jéssica Alves Medeiros de Araújo, Diego Marques‐Coelho, Loyal A. Goff, Marcos Romualdo Costa, Ulrich Müller, Cristina Gil-Sanz
Software Mentions: 2
Published: about 3 years ago
10.21451/1984-3143-AR2019-0001
Evaluation of the proteomic profiles of ejaculated spermatozoa from Saanen bucks (Capra hircus)Cited by: 4
Author(s): Tatiana Maria Farias Pinto, Raulzito Fernandes Moreira, Maria Nágila Carneiro Matos, Vitória Virgínia Magalhães Soares, Mônica Valéria de Almeida Aguiar, Paulo de Tarso Teles Dourado de Aragão, João Garcia Alves, Frederico Bruno Mendes Batista Moreno, Ana Cristina de Oliveira Monteiro‐Moreira, Cíntia Renata Rocha Costa, José Luiz de Lima, Â. M. X. Eloy, Rodrigo Maranguape Silva da Cunha
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0082457
Reverse Engineering the Neuroblastoma Regulatory Network Uncovers MAX as One of the Master Regulators of Tumor ProgressionCited by: 13
Author(s): Ricardo D’Oliveira Albanus, Rodrigo Juliani Siqueira Dalmolin, Mauro A. A. Castro, Matheus Augusto de Bittencourt Pasquali, Vitor de Miranda Ramos, Daniel Pens Gelain, José Cláudio Fonseca Moreira
Software Mentions: 2
Published: over 10 years ago
10.3389/fcell.2020.00492
Identification of Prognostic Biomarkers for Multiple Solid Tumors Using a Human Villi Development ModelCited by: 9
Author(s): Botao Zhang, Zhengliang Wang, Hongxia Li, Feng Li, Wenbin Li, Shujun Cheng
Software Mentions: 2
Published: about 4 years ago
10.3390/ijms20143444
Long Non-coding RNAs as Important Biomarkers in Laryngeal Cancer and Other Head and Neck TumoursCited by: 61
Author(s): Alessia Maria Cossu, Laura Mosca, Silvia Zappavigna, Gabriella Misso, Marco Bocchetti, Federica De Micco, Lucio Quagliuolo, Marina Porcelli, Michele Caraglia, Mariarosaria Boccellino
Software Mentions: 2
Published: about 5 years ago
10.1038/s41419-018-1183-8
Long noncoding RNA AC003092.1 promotes temozolomide chemosensitivity through miR-195/TFPI-2 signaling modulation in glioblastomaCited by: 57
Author(s): Ningbo Xu, Boyang Liu, Changlin Lian, Desislava Doycheva, Fen Zhao, Yanting Liu, Jian Zhou, Zhenyan He, Yang Zhao, Qiongzhen Huang, Huijun Zeng
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0093271
An Analysis of the Global Expression of MicroRNAs in an Experimental Model of Physiological Left Ventricular HypertrophyCited by: 49
Author(s): Nidiane Carla Martinelli, Carolina Rodrigues Cohen, Kátia Gonçalves dos Santos, Mauro A. A. Castro, Andréia Biolo, Luzia Menegotto Frick, Daiane Silvello, Amanda Lopes, S Schneider, Michael Éverton Andrades, Nadine Oliveira Clausell, Úrsula da Silveira Matte, Luís Eduardo Paim Rohde
Software Mentions: 1
Published: over 10 years ago
10.1186/gb-2013-14-10-r118
Temporal dynamics and transcriptional control using single-cell gene expression analysisCited by: 46
Author(s): Tsukasa Kouno, Michiel de Hoon, Jessica C. Mar, Yuji Tomaru, Mitsuoki Kawano, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki, Jay W. Shin
Software Mentions: 1
Published: over 11 years ago