Abstract
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.
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
- EXTJS
- 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
- 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
- Thn
- naïve T helper cells
- UCSC
- University of California, Santa Cruz
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.