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Omics BioAnalytics: Reproducible Research using R Shiny and Alexa [article]

Amrit Singh, Scott J Tebbutt, Bruce M McManus
2020 bioRxiv   pre-print
Blending web-based (R Shiny) and voice-based (Amazon's Alexa) analytics, Omics BioAnalytics can be deployed both by expert computational biologists and non-coding biological domain experts, alike.  ...  Well-designed web frameworks enable more intuitive and efficient analysis such that less time is spent on coding and more time is spent on interpretation of results and addressing insightful biological  ...  The R Shiny framework is being heavily leveraged in 3 5 developing interactive web apps for high-throughput omics data (e.g.  ... 
doi:10.1101/2020.05.05.024323 fatcat:mq25uksux5bf5ghtcu2jjh72vu

V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data

2020 Bioinformatics  
To facilitate the interpretation of surrogate variables detected by algorithms including IA-SVA, SVA, or ZINB-WaVE, we developed an R Shiny application (Visual Surrogate Variable Analysis (V-SVA)) that  ...  This interactive framework includes tools for discovery of genes associated with detected sources of variation, gene annotation using publicly available databases and gene sets, and data visualization  ...  To address this challenge, we developed an R Shiny (Chang et al., 2018) application for Visual Surrogate Variable Analysis (V-SVA).  ... 
doi:10.1093/bioinformatics/btaa128 pmid:32119082 pmcid:PMC7267827 fatcat:v7cpkfsrwjhmhg5n3ncsldkbxa

ChromSCape : an R/Shiny application for interactive analysis of single-cell chromatin profiles [article]

Pacôme Prompsy, Pia Kirchmeier, Céline Vallot
2019 bioRxiv   pre-print
With these methods, we can detect the heterogeneity of epigenomic profiles within complex biological samples.  ...  Here, we present ChromSCape: a user-friendly Shiny/R application that processes single-cell epigenomic data to help the biological interpretation of epigenomic landscapes within cell populations.  ...  Overall, we predict that ChromSCape will be a useful tool to probe heterogeneity and dynamics of chromatin profiles in various biological settings, not only in cancer development but also in cell development  ... 
doi:10.1101/683037 fatcat:urliqpmhgrakrkdtonro4ix5sq

iGEAK: an interactive gene expression analysis kit for seamless workflow using the R/shiny platform

Kwangmin Choi, Nancy Ratner
2019 BMC Genomics  
Results: iGEAK is an R/Shiny-based client-side desktop application, providing an interactive gene expression data analysis pipeline for microarray and RNA-seq data.  ...  To avoid bottlenecks impeding seamless analysis processing, we have developed an Interactive Gene Expression Analysis Kit, we term iGEAK, focusing on usability and interactivity. iGEAK is designed to be  ...  Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.  ... 
doi:10.1186/s12864-019-5548-x fatcat:633vsbjrs5e2zlsi6tocjqgkfa

CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network

Xiao Wen, Lin Gao, Tuo Song, Chaoqun Jiang
2021 BMC Bioinformatics  
CeNet Omnibus is an R/Shiny application based on the Shiny framework developed by RStudio.  ...  To fill this gap, we introduce CeNet Omnibus, an R/Shiny application, which provides a unified framework for the construction and analysis of ceRNA network.  ...  Acknowledgements The authors would like to thank Ran Duan and Peizhuo Wang for discussion about the design of the web page and test of the programs.  ... 
doi:10.1186/s12859-021-04012-y pmid:33602117 fatcat:clp4lhyzrfcphnlqzqqpu6six4

shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes

Yiming Yu, Wen Yao, Yuping Wang, Fangfang Huang
2020 Genomics, Proteomics & Bioinformatics  
To address these issues, we developed a new R/Shiny application, named shinyChromosome, as a GUI for the interactive creation of non-circular whole genome diagrams. shinyChromosome can be easily installed  ...  Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.  ...  Acknowledgments This study was supported by the research start-up fund to topnotch talents of Henan Agricultural University (Grant No. 30500581), China.  ... 
doi:10.1016/j.gpb.2019.07.003 pmid:31931182 pmcid:PMC7056921 fatcat:bbbfnbvirvcnhfd7xernzyxqfy

TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs

Peter Zhang, Alida Palmisano, Ravindra Kumar, Ming-Chung Li, James H Doroshow, Yingdong Zhao, Pier Luigi Martelli
2021 Bioinformatics  
We developed "TPWshiny" as a standalone, easy to install, R application to facilitate more interactive data exploration.  ...  The NCI TPW data are publicly available through a web interface that allows limited user interaction with the data.  ...  Here we present an R/Shiny application package providing convenient access to NCI TPW data, with effective visualization tools for interactive use.  ... 
doi:10.1093/bioinformatics/btab619 fatcat:unim7wvtunhnzcmwto4n43roqy

MOPower: an R-shiny application for the simulation and power calculation of multi-omics studies [article]

Hamzah Syed, Georg W Otto, Daniel Kelberman, Chiara Bacchelli, Philip L Beales
2021 bioRxiv   pre-print
Results: The interactive R shiny application MOPower described below simulates data based on three different omics using statistical distributions.  ...  Methods development for multi-omics studies is in its early stages due to the complexity of the different individual data types.  ...  Acknowledgements The authors wish to thank the entire GOSgene team at the Institute of Child Health UCL, for their assistance in testing and providing feedback on MOPower.  ... 
doi:10.1101/2021.12.19.473339 fatcat:tb2kcuau7nayhbqhqdszotd65e

ceRNAshiny: An Interactive R/Shiny App for Identification and Analysis of ceRNA Regulation

Yueqiang Song, Jia Li, Yiming Mao, Xi Zhang
2022 Frontiers in Molecular Biosciences  
To fill this gap, we developed ceRNAshiny, an interactive R/Shiny application, which integrates widely used computational methods and databases to provide and visualize the construction and analysis of  ...  Besides, the conventional tools were mainly devoted to investigating ceRNAs in malignancies instead of those in neurodegenerative diseases.  ...  Meanwhile, the newly developed CeNet Omnibus, an R/Shiny-based application, is used to predict ceRNA network construction using different computational methods (Wen et al., 2021) with database information  ... 
doi:10.3389/fmolb.2022.865408 pmid:35647026 pmcid:PMC9136144 fatcat:ss3yejmtr5a6tetkb5noadbmgy

CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer

Rebecca G Ramesh, Ashkan Bigdeli, Chase Rushton, Jason N Rosenbaum
2022 Journal of Pathology Informatics  
CNViz is a freely accessible R/Bioconductor package that launches an interactive R/Shiny visualization tool to facilitate review of copy number data.  ...  An example of the application is available at rebeccagreenblatt.shinyapps.io/cnviz_example.  ...  Shiny is an R package that enables the creation of interactive web applications within the R environment, allowing the developer to take advantage of many open source data manipulation and bioinformatics  ... 
doi:10.1016/j.jpi.2022.100089 pmid:35251754 pmcid:PMC8888957 fatcat:qyaf2ljlhfg6bmgxnbd3wpmyji

SEQUIN: rapid and reproducible analysis of RNA-seq data in R/Shiny [article]

Claire Weber, Marissa B Hirst, Ben Ernest, Hannah Baskir, Carlos A Tristan, Pei-Hsuan Chu, Ilyas Singec
2022 bioRxiv   pre-print
SEQUIN is a new web application (app) that allows fast and intuitive RNA-sequencing data analysis for organisms, tissues, and single cells.  ...  Freely available to the public, SEQUIN empowers scientists to investigate transcriptome data firsthand with cutting edge statistical methods.  ...  While it is possible to load upwards of 100,000 cells into R, this will cause problems in R/Shiny.  ... 
doi:10.1101/2022.02.23.481646 fatcat:rhtfpz5abfdmjdt6d2lfow5xxq

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information

Elly Poretsky, Alisa Huffaker
2020 PeerJ  
To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses.  ...  , the application is uncommonly used to drive new pathway discoveries.  ...  Towards this goal, we developed an R Shiny web-application, termed MutRank, to facilitate user control over both targeted and non-targeted MR-based coexpression analyses for rapid hypothesis testing.  ... 
doi:10.7717/peerj.10264 pmid:33240618 pmcid:PMC7659623 fatcat:x2s5lpo7ircnrk7ogp4krynnam

MINOTAUR: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny [article]

Robert Verity, Caitlin Collins, Daren C. Card, Sara M Schaal, Liuyang Wang, Kathleen Lotterhos
2016 bioRxiv   pre-print
These metrics are implemented in the R package MINOTAUR, which also includes an interactive web-based application for visualizing outliers in high-dimensional datasets.  ...  Genome scans are widely used to identify 'outliers' in genomic data: loci with different patterns compared with the rest of the genome due to the action of selection or other non-adaptive forces of evolution  ...  such as the R Shiny and Shiny Dashboard environments (Chang 371 2015; Chang et al. 2016) dramatically aid in the development of R-based user-friendly 372 390 Development: 390 The development of MINOTAUR  ... 
doi:10.1101/062158 fatcat:jlujzbhwejhw5dwntgypsz5pvu

KRSA: An R package and R Shiny web application for an end-to-end upstream kinase analysis of kinome array data

Erica A. K. DePasquale, Khaled Alganem, Eduard Bentea, Nawshaba Nawreen, Jennifer L. McGuire, Tushar Tomar, Faris Naji, Riet Hilhorst, Jaroslaw Meller, Robert E. McCullumsmith, Stephen D. Ginsberg
2021 PLoS ONE  
We present Kinome Random Sampling Analyzer (KRSA), an R package and R Shiny web-application for analyzing kinome array data to help users better understand the patterns of functional proteomics in complex  ...  biological systems.  ...  We also thank the developers of R studio, Shiny, and supporting R packages used in the implementation of KRSA.  ... 
doi:10.1371/journal.pone.0260440 pmid:34919543 pmcid:PMC8682895 fatcat:dc224qxloff23oatjxkvndnbga

Methylscaper: an R/shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data

Parker Knight, Marie-Pierre L Gauthier, Carolina E Pardo, Russell P Darst, Kevin Kapadia, Hadley Browder, Eliza Morton, Alberto Riva, Michael P Kladde, Rhonda Bacher, Peter Robinson
2021 Bioinformatics  
Summary Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer.  ...  In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btab438 pmid:34125875 pmcid:PMC8665741 fatcat:m7tnqvjkurfm3ckkcakov2rzza
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