title: CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.
abstract: BACKGROUND
  Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers.
  
  
  RESULTS
  To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app .
  
  
  CONCLUSIONS
  We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.
authors.affiliation: Department of Psychiatry, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. dvelmeshev@med.miami.edu.|Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. dvelmeshev@med.miami.edu.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Velmeshev
authors.affiliation: Department of Psychiatry, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. p.lally1@umiami.edu.|Department of Biomedical Engineering, University of Miami, Coral Gables, FL, 33146, USA. p.lally1@umiami.edu.
authors.forename: Patrick
authors.initials: P
authors.lastname: Lally
authors.affiliation: Department of Psychiatry, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. mmagistri@med.miami.edu.
authors.forename: Marco
authors.initials: M
authors.lastname: Magistri
authors.affiliation: Department of Psychiatry, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. MFaghihi@med.miami.edu.
authors.forename: Mohammad Ali
authors.initials: MA
authors.lastname: Faghihi
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D012313:RNA / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface
chemical_list: D012313:RNA