BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data¶
Andrey V. Kartashov, Artem Barski
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Development of next-generation sequencing has revolutionized molecular biology by enhancing the ability to perform genome-wide studies. However, due to the need for bioinformatic expertise and the size of resulting datasets, use of these technologies is still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe Experiment Management System, which allows users to store, visualize and analyze epigenomic and transcriptomic next-generation sequencing data using a biologist-friendly, web-based graphical user interface without the need for programming expertize. BioWardrobe can be installed on consumer-class hardware within an institutional local network. Analysis capabilities include predefined pipelines that allow the user to download data from either institutional core facilities or public databases, perform quality control, map reads and visualize data on a built-in mirror of the University of California, Santa Cruz (UCSC) genome browser. Reads per kilobase of transcript per million reads mapped (RPKMs) are calculated for RNA sequencing (RNA-Seq), and islands of enrichment are identified for chromatin immunoprecipitation sequencing (ChIP-Seq) and similar datasets. Advanced analysis capabilities include analyzing differential gene expression and binding and creating average tag density profiles and heatmaps. ...
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