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