Autoren:	Marini, Federico Binder, Harald
Titel:	pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Online-Publikationsdatum:	8-Nov-2019
Erscheinungsdatum:	2019
Sprache des Dokuments:	Englisch
Zusammenfassung/Abstract:	Background Principal component analysis (PCA) is frequently used in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking. Results We developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny framework and exploits data structures from the open-source Bioconductor project. Users can easily generate a wide variety of publication-ready graphs, while assessing the expression data in the different modules available, including a general overview, dimension reduction on samples and genes, as well as functional interpretation of the principal components. Conclusion pcaExplorer is distributed as an R package in the Bioconductor project (http://bioconductor.org/packages/pcaExplorer/), and is designed to assist a broad range of researchers in the critical step of interactive data exploration.
DDC-Sachgruppe:	610 Medizin 610 Medical sciences
Veröffentlichende Institution:	Johannes Gutenberg-Universität Mainz
Organisationseinheit:	FB 04 Medizin
Veröffentlichungsort:	Mainz
ROR:	https://ror.org/023b0x485
DOI:	http://doi.org/10.25358/openscience-219
Version:	Published version
Publikationstyp:	Zeitschriftenaufsatz
Nutzungsrechte:	CC BY
Informationen zu den Nutzungsrechten:	https://creativecommons.org/licenses/by/4.0/
Zeitschrift:	BMC bioinformatics 20
Seitenzahl oder Artikelnummer:	Art. 331
Verlag:	BioMed Central
Verlagsort:	London
Erscheinungsdatum:	2019
ISSN:	1471-2105
URL der Originalveröffentlichung:	http://dx.doi.org/10.1186/s12859-019-2879-1
DOI der Originalveröffentlichung:	10.1186/s12859-019-2879-1
Enthalten in den Sammlungen:	JGU-Publikationen