TY - JOUR T1 - Wardrobe - an integrated system for analysis of epigenomics and transcriptomics data JF - bioRxiv DO - 10.1101/012799 SP - 012799 AU - Andrey V. Kartashov AU - Artem Barski Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/12/22/012799.abstract N2 - High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, technologies are still beyond the capabilities of many laboratories. Herein, we present Wardrobe server, which allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly GUI without the need for programming expertise. Predefined pipelines allow users to download data from core facilities or public databases, visualize data on a genome browser, calculate RPKMs and identify islands. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag density profiles and heatmaps. Wardrobe code is available at https://code.google.com/p/genome-tools/.A limited functionality demo-version is available at http://demo.wardrobe.porter.st.ATAC-Seqassay for transposase-accessible chromatin sequencingChIPchromatin immunoprecipitationChIP-Seqchromatin immunoprecipitation sequencingD3data-driven documentsDNase-SeqDNase I hypersensitive sites sequencingExt JSextension JavaScriptftpfile transfer protocolGEOGene Expression OmnibusGRO-Seqglobal run-on sequencingHIPAAHealth Insurance Portability and Accountability Act of 1996HTMLhypertext markup languageMACSmodel-based analysis of ChIP-SeqMAnorma model for quantitative comparison of ChIP-Seq datasetsMe3trimethylationMNase-Seqmicrococcal nuclease sequencingMWWMann-Whitney-WilcoxonNGSnext-generation sequencingPHPPHP: hypertext preprocessorRAMrandom-access memoryRefSeqNational Center for Biotechnology Information Reference SequenceRPKMsreads per kilobase of transcript per million reads mappedRNA-Seqribonucleic acid sequencingSATA HDDserial ATA hard disk driveSRASequence Read Archive (formerly known as Short Read Archive)STARspliced transcripts alignment to a referenceSVGscalable vector graphicsTSStranscription start site(s)Th1T helper type 1ThpT helper precursor cellsUCSCUniversity of California, Santa Cruz ER -