SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: Picking ChIP-seq peak detectors for analyzing chromatin modification experi Newsbot! Literature Watch 1 06-14-2012 04:31 AM
ChIP-Seq: PRI-CAT: a web-tool for the analysis, storage and visualization of plant Ch Newsbot! Literature Watch 0 05-26-2011 02:10 AM
Transcription factors visualization tool for chip seq data shum1 General 0 05-03-2010 07:29 AM

Reply
 
Thread Tools
Old 09-07-2013, 08:20 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,439
Default ChIP-Seq: PAVIS: a tool for Peak Annotation and Visualization.

Syndicated from PubMed RSS Feeds

PAVIS: a tool for Peak Annotation and Visualization.

Bioinformatics. 2013 Sep 4;

Authors: Huang W, Loganantharaj R, Schroeder B, Fargo D, Li L

Abstract
SUMMARY: We introduce a web-based tool, Peak Annotation and Visualization (PAVIS), for annotating and visualizing ChIP-seq peak data. PAVIS is designed with non-bioinformaticians in mind and presents a straightforward user interface to facilitate biological interpretation of ChIP-seq peak or other genomic enrichment data. PAVIS, through association with annotation, provides relevant genomic context for each peak, such as peak location relative to genomic features including transcription start site, intron, exon, or 5'/3' -UTR. PAVIS reports the relative enrichment p-values of peaks in these functionally distinct categories, and provides a summary plot of the relative proportion of peaks in each category. PAVIS, unlike many other resources, provides a peak-oriented annotation and visualization system, allowing dynamic visualization of tens to hundreds of loci from one or more ChIP-seq experiments, simultaneously. PAVIS enables rapid, and easy examination and cross-comparison of the genomic context and potential functions of the underlying genomic elements thus supporting downstream hypothesis generation.
AVAILABILITY: PAVIS is publicly accessed at http://manticore.niehs.nih.gov/pavis.
CONTACT: li3@niehs.nih.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


PMID: 24008416 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO