TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota

ABSTRACT

OBJECTIVE: Differential expression (DE) is a fundamental step in the analysis of RNA-Seq count data. We had previously developed an R/Bioconductor package (called TCC) for this purpose. While this package has the unique feature of an in-built robust normalization method, its use has so far been limited to R users only. There is thus, a need for an alternative to DE analysis by TCC for non-R users. RESULTS: Here, we present a graphical user interface for TCC (called TCC-GUI). Non-R users only need a web browser as the minimum requirement for its use ( https://infinityloop.shinyapps.io/TCC-GUI/ ). TCC-GUI is implemented in R and encapsulated in Shiny application. It contains all the major functionalities of TCC, including DE pipelines with robust normalization and simulation data generation under various conditions. It also contains (i) tools for exploratory analysis, including a useful score termed average silhouette that measures the degree of separation of compared groups, (ii) visualization tools such as volcano plot and heatmap with hierarchical clustering, and (iii) a reporting tool using R Markdown. By virtue of the Shiny-based GUI framework, users can obtain results simply by mouse navigation. The source code for TCC-GUI is available at https://github.com/swsoyee/TCC-GUI under MIT license. More... »

PAGES

133

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13104-019-4179-2

DOI

http://dx.doi.org/10.1186/s13104-019-4179-2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112739231

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30867032


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