PT - JOURNAL ARTICLE AU - Andrey V. Kartashov AU - Artem Barski TI - BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data AID - 10.1101/012799 DP - 2015 Jan 01 TA - bioRxiv PG - 012799 4099 - http://biorxiv.org/content/early/2015/04/20/012799.short 4100 - http://biorxiv.org/content/early/2015/04/20/012799.full AB - BioWardrobe is an integrated platform that empowers users to store, visualize and analyze epigenomics and transcriptomics data, without the need for programming expertise, by using a biologist-friendly webbased user interface. Predefined pipelines automate download of data from core facilities or public databases, calculate RPKMs and identify peaks and display results via the interactive web interface. Additional capabilities include analyzing differential gene expression and DNA-protein binding and creating average tag density profiles and heatmaps.ATAC-Seqassay for transposase-accessible chromatin sequencingChIPchromatin immunoprecipitationChIP-Seqchromatin immunoprecipitation sequencingD3data-driven documentsDNase-SeqDNase I hypersensitive sites sequencingEXTJSextension 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 datasetsMNase-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 1Thnnaïve T helper cellsUCSCUniversity of California, Santa Cruz