Home

  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 is open source and released under the terms of the GNU General Public License v2 (GPL).

 

Documentation

• Installing BioWardrobe
• Administration Guide
• User Guide
• Developer Guide

Publications

• Kartashov, Andrey V., and Artem Barski. “BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data.” Genome Biology 16.1 (2015): 158.
  Journal

• Vallabh,S., Kartashov,A. V. and Barski,A. (2018) Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe. Methods Mol. Biol., 1783, 343–360.
  Journal
• Papers using BioWardrobe in PubMed

Features

• Universal experiment entry form
• Fully automated Basic analysis
  • Mapping NGS data by Bowtie / STAR
  • Quality Control
    • FASTX-Toolkit
    • Base Frequency/QC plot
    • Alignment Statistics
  • Calculating RPKMs for RNAs (source:src/reads-counting)
  • Finding islands of enrichment for ChIPs with MACS2 each island assigned to a gene and region upstream/promoter/exon/intron/intergenic
    • Islands distribution plot by regions
    • Dynamic data filtering
    • Nucleotide sequence of islands can be saved in fasta format
  • Upload to the local copy of UCSC genome browser
  • Customizable analysis with R: default and custom/editable R
• User-directed Advanced analysis
  • Differential gene expression analysis with DESeq / DESeq2
  • Differential binding analysis MANorm
  • Average Tag Density Profile plots (source:src/atdp) are available
    • Around TSS
    • Gene body coverage
  • Heatmaps
  • R data processing
    • PCA
    • IDR

Online demo

  In this demo https://demo.biowardrobe.com/ BioWardrobe functionality has been limited due to space and computational power constraints. Unlike the full version, users can not create new accounts or folders, cannot download new datasets and cannot run new analysis. However, users can view the datasets already there and view the results of analysis described in our paper. There are 3 accounts/passwords admin/admin, user/user, guest/guest with admin/local admin/worker privileges.

Virtual Machine

VirtualBox image is provided for those who would like to try BioWardrobe without a hassle of actually installing it.

  VirtualBox Instructions

Support & getting help

For getting help or discussing about BioWardrobe, you can browse the BioWardrobe Issues.