Summary: The package mvlearnR and accompanying Shiny App is intended for integrating data from multiple sources or views or modalities (e.g. genomics, proteomics, clinical, and demographic data). Most existing software packages for multiview learning are decentralized and offer limited capabilities, making it difficult for users to perform comprehensive integrative analysis. The new package wraps statistical and machine learning methods and graphical tools, providing a convenient and easy data integration workflow. For users with limited programming language, we provide a Shiny Application to facilitate data integration anywhere and on any device. The methods have potential to offer deeper insights into complex disease mechanisms.
Availability And Implementation: mvlearnR is available from the following GitHub repository: https://github.com/lasandrall/mvlearnR. The web application is hosted on shinyapps.io and available at: https://multi-viewlearn.shinyapps.io/MultiView_Modeling/.
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http://dx.doi.org/10.1093/bioadv/vbae005 | DOI Listing |
BMC Med Res Methodol
January 2025
Biostatistics Research Group, Department of Population Health Sciences, University of Leicester, Leicester, UK.
Background: Since 2015, the Complex Reviews Synthesis Unit (CRSU) has developed a suite of web-based applications (apps) that conduct complex evidence synthesis meta-analyses through point-and-click interfaces. This has been achieved in the R programming language by combining existing R packages that conduct meta-analysis with the shiny web-application package. The CRSU apps have evolved from two short-term student projects into a suite of eight apps that are used for more than 3,000 h per month.
View Article and Find Full Text PDFBMC Genomics
January 2025
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
Motivation: Next-generation sequencing technologies, such as whole genome sequencing (WGS), have become prominent in cancer genomics. However, managing, visualizing, and integratively analyzing WGS results across various bioinformatic pipelines remains challenging, particularly for non-bioinformaticians, hindering the usability of WGS data for biological discovery.
Results: We developed Sherlock-Genome, an R Shiny app for data harmonization, visualization, and integrative analysis of WGS-based cancer genomics studies.
Circ Cardiovasc Qual Outcomes
January 2025
Department of Cardiothoracic Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands. (X.W., M.L.N., K.M.V., P.G., J.R.G.E., A.J.J.C.B., J.J.M.T.).
Background: Observed patient survival after cardiothoracic interventions should ideally be placed in the context of matched-general-population survival. This study outlines several methodologies of matching general population mortality to the study sample, subsequently calculating cumulative matched-general-population survival, highlighting their respective advantages, disadvantages, and limitations.
Methods: A multicenter data set containing survival data after the Ross procedure was used for methodological illustration.
Behav Res Methods
January 2025
Educational Sciences, Child Development and Education, University of Amsterdam, Amsterdam, The Netherlands.
J R Soc Interface
January 2025
IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France.
Contact tracing is commonly used to manage infectious diseases of both humans and animals. It aims to detect early and control potentially infected individuals or farms that had contact with infectious cases. Because it is very resource-intensive, contact tracing is usually performed on a pre-defined time window, based on previous knowledge of the duration of the incubation period.
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