title: RPPApipe: a pipeline for the analysis of reverse-phase protein array data.
abstract: OBJECTIVE
  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.
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany. Electronic address: johannes.eichner@uni-tuebingen.de.
authors.forename: Johannes
authors.initials: J
authors.lastname: Eichner
authors.affiliation: Natural and Medical Sciences Institute at the University of Tuebingen (NMI), Reutlingen 72770, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Heubach
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ruff
authors.affiliation: 4SC AG, Planegg-Martinsried 82152, Germany.
authors.forename: Hella
authors.initials: H
authors.lastname: Kohlhof
authors.affiliation: 4SC AG, Planegg-Martinsried 82152, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Strobl
authors.affiliation: SpheroTec GmbH, Planegg-Martinsried 82152, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Mayer
authors.affiliation: Natural and Medical Sciences Institute at the University of Tuebingen (NMI), Reutlingen 72770, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Pawlak
authors.affiliation: Natural and Medical Sciences Institute at the University of Tuebingen (NMI), Reutlingen 72770, Germany.
authors.forename: Markus F
authors.initials: MF
authors.lastname: Templin
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Zell
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D020407:Internet; D040081:Protein Array Analysis / Q000379:methods*; D012984:Software
keywords: Clustering; Pathway analysis; Reverse-phase protein arrays; Statistical analysis; Visualization; Web application