Background and scope: Today, web-based data analysis pipelines
exist for a wide variety of microarray platforms, such as ordinary
gene-centered arrays, exon arrays and SNP arrays. However, most of the
available software tools provide only limited support for reverse-phase
protein arrays (RPPA), as relevant inherent properties of the corresponding
datasets are not taken into account. Thus, we developed the web-based data
analysis pipeline RPPApipe, which was specifically tailored to suit the
characteristics of the RPPA platform and encompasses various tools for data
preprocessing, statistical analysis, clustering and pathway analysis.
Implementation and performance: All tools which are part of the RPPApipe
software were implemented using R/Bioconductor. The software was embedded
into our web-based ZBIT Bioinformatics Toolbox which is a customized
instance of the Galaxy platform.
Availability: RPPApipe is freely available under GNU Public License from
http://webservices.cs.uni-tuebingen.de. A full documentation of the
tool can be found on the corresponding website
http://www.cogsys.cs.uni-tuebingen.de/software/RPPApipe.
© 2014 Elsevier Ireland Ltd.
@article{Eichner2014c, author = {Eichner, Johannes and Heubach, Yvonne and Ruff, Manuel and Kohlhof, Hella and Strobl, Stefan and Mayer, Barbara and Pawlak, Michael and Templin, Markus F. and Zell, Andreas}, title = {{RPPApipe: A pipeline for the analysis of reverse-phase protein array data}}, journal = {BioSystems}, year = {2014}, month = jun, keywords = {Reverse-phase protein arrays; Web application; Statistical analysis; Clustering; Pathway analysis; Visualization}, abstract = {Background and scope: Today, web-based data analysis pipelines exist for a wide variety of microarray platforms, such as ordinary gene-centered arrays, exon arrays and SNP arrays. However, most of the available software tools provide only limited support for reverse-phase protein arrays (RPPA), as relevant inherent properties of the corresponding datasets are not taken into account. Thus, we developed the web-based data analysis pipeline RPPApipe, which was specifically tailored to suit the characteristics of the RPPA platform and encompasses various tools for data preprocessing, statistical analysis, clustering and pathway analysis. Implementation and performance: All tools which are part of the RPPApipe software were implemented using R/Bioconductor. The software was embedded into our web-based ZBIT Bioinformatics Toolbox which is a customized instance of the Galaxy platform. Availability: RPPApipe is freely available under GNU Public License from \url{http://webservices.cs.uni-tuebingen.de}. A full documentation of the tool can be found on the corresponding website \url{http://www.cogsys.cs.uni-tuebingen.de/software/RPPApipe}. \textcopyright{} 2014 Elsevier Ireland Ltd.}, doi = {10.1016/j.biosystems.2014.06.009}, url = {http://www.sciencedirect.com/science/article/pii/S0303264714000902}, pdf = {http://www.sciencedirect.com/science/article/pii/S0303264714000902/pdfft?md5=8824813e798bbc740be6b96c29e944e2&pid=1-s2.0-S0303264714000902-main.pdf}, publisher = {Elsevier}, }