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: MultiAssayExperiment

https://packages.ecosyste.ms/registries/bioconductor.org/packages/MultiAssayExperiment

Software for the integration of multi-omics experiments in Bioconductor
1 version
Latest release: 10 months ago
53 dependent packages
184,742 downloads total

Papers Mentioning MultiAssayExperiment 16

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

10.12688/f1000research.15666.3

A systematic performance evaluation of clustering methods for single-cell RNA-seq data
Cited by: 33
Author(s): Angelo Duò, Mark D. Robinson, Charlotte Soneson
Software Mentions: 17
Published: over 3 years ago

10.3390/ijms22062822

A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research
Cited by: 6
Author(s): Efstathios Iason Vlachavas, Jonas Bohn, Frank Ückert, Sylvia Nürnberg
Software Mentions: 16
Published: over 3 years ago

10.1038/s41598-021-81200-z

MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studies
Cited by: 11
Author(s): Mario Zanfardino, Rossana Castaldo, Katia Pane, Ornella Affinito, Marco Aiello, Marco Salvatore, Monica Franzese
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-016-1455-1

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
Cited by: 20
Author(s): Carles Hernández-Ferrer, Carlos Ruiz‐Arenas, Alba Beltran-Gomila, Juan R. González
Software Mentions: 14
Published: over 7 years ago

10.12688/f1000research.8900.2

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
Cited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: over 7 years ago

10.3390/ijms22115751

Multi-Omics Model Applied to Cancer Genetics
Cited by: 14
Author(s): Francesco Pettini, Anna Visibelli, Vittoria Cicaloni, Daniele Iovinelli, Ottavia Spiga
Software Mentions: 14
Published: about 3 years ago

10.1186/s40168-021-01013-0

animalcules: interactive microbiome analytics and visualization in R
Cited by: 16
Author(s): Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti, W. Evan Johnson
Software Mentions: 7
Published: over 3 years ago

10.1186/s12967-019-2073-2

Bringing radiomics into a multi-omics framework for a comprehensive genotype–phenotype characterization of oncological diseases
Cited by: 63
Author(s): Mario Zanfardino, Monica Franzese, Katia Pane, Carlo Cavaliere, Serena Monti, Giuseppina Esposito, Marco Salvatore, Marco Aiello
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12859-018-2344-6

Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data
Cited by: 32
Author(s): Simon Klau, Vindi Jurinović, Roman Hornung, Tobias Herold, Anne‐Laure Boulesteix
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pcbi.1009131

MiDAS—Meaningful Immunogenetic Data at Scale
Cited by: 9
Author(s): Maciej Migdał, Dan Fu Ruan, William F. Forrest, Amir Horowitz, Christian Hammer
Software Mentions: 4
Published: about 3 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: over 3 years ago

10.1200/CCI.19.00111

Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale
Cited by: 3
Author(s): Vincent J. Carey, Marcel Ramos, Benjamin J. Stubbs, Shweta Gopaulakrishnan, Sehyun Oh, Nitesh Turaga, Levi Waldron, Martin Morgan
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.xcrm.2020.100078

Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19
Cited by: 147
Author(s): Lucie Rodriguez, Pirkka T. Pekkarinen, Tadepally Lakshmikanth, Ziyang Tan, Camila Rosat Consiglio, Christian Pou, Yang Chen, Constantin Habimana Mugabo, Ngoc-anh A. Nguyen, Kirsten Nowlan, Tomas Strandin, Lev Levanov, Jaromír Mikes, Wang Ju, Anu Kantele, Jussi Hepojoki, Olli Vapalahti, Santtu Heinonen, Eliisa Kekäläinen, Petter Brodin
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-021-02433-9

Community-wide hackathons to identify central themes in single-cell multi-omics
Cited by: 6
Author(s): Kim‐Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, P. Jeganathan, Melanie Loth, Chen Meng, Wancen Mu, Véra Pancaldi, Kris Sankaran, Dario Righelli, Amrit Singh, Joshua Sodicoff, Genevieve Stein-O’Brien, Ayshwarya Subramanian, Joshua D. Welch, Yue You, Ricard Argelaguet, Vincent J. Carey, Ruben Dries, Casey S. Greene, Susan Holmes, Michael I. Love, Matthew E. Ritchie, Guo‐Cheng Yuan, Aedín Culhane, Elana J. Fertig
Software Mentions: 2
Published: almost 3 years ago

10.1128/mSystems.00194-17

Data and Statistical Methods To Analyze the Human Microbiome
Cited by: 11
Author(s): Levi Waldron
Software Mentions: 1
Published: over 6 years ago