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BMC Res Notes. 2019 Mar 13;12(1):133. doi: 10.1186/s13104-019-4179-2.

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

Author information

1
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
2
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
3
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. kadota@bi.a.u-tokyo.ac.jp.
4
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. kadota@bi.a.u-tokyo.ac.jp.

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.

KEYWORDS:

Bioinformatics; Differential expression analysis; RNA-Seq; Shiny app

PMID:
30867032
PMCID:
PMC6417217
DOI:
10.1186/s13104-019-4179-2
[Indexed for MEDLINE]
Free PMC Article

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