Abstract
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.
List of abbreviations used
- ATAC-Seq
- assay for transposase-accessible chromatin sequencing
- ChIP
- chromatin immunoprecipitation
- ChIP-Seq
- chromatin immunoprecipitation sequencing
- D3
- data-driven documents
- DNase-Seq
- DNase I hypersensitive sites sequencing
- Ext JS
- extension JavaScript
- ftp
- file transfer protocol
- GEO
- Gene Expression Omnibus
- GRO-Seq
- global run-on sequencing
- HIPAA
- Health Insurance Portability and Accountability Act of 1996
- HTML
- hypertext markup language
- MACS
- model-based analysis of ChIP-Seq
- MAnorm
- a model for quantitative comparison of ChIP-Seq datasets
- Me3
- trimethylation
- MNase-Seq
- micrococcal nuclease sequencing
- MWW
- Mann-Whitney-Wilcoxon
- NGS
- next-generation sequencing
- PHP
- PHP: hypertext preprocessor
- RAM
- random-access memory
- RefSeq
- National Center for Biotechnology Information Reference Sequence
- RPKMs
- reads per kilobase of transcript per million reads mapped
- RNA-Seq
- ribonucleic acid sequencing
- SATA HDD
- serial ATA hard disk drive
- SRA
- Sequence Read Archive (formerly known as Short Read Archive)
- STAR
- spliced transcripts alignment to a reference
- SVG
- scalable vector graphics
- TSS
- transcription start site(s)
- Th1
- T helper type 1
- Thp
- T helper precursor cells
- UCSC
- University of California, Santa Cruz