SEQanswers

Go Back   SEQanswers > Applications Forums > Epigenetics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: Enabling Data Analysis on High-Throughput Data in Large Data Depository Usi Newsbot! Literature Watch 1 04-18-2018 10:50 PM
ChIP-Seq: ChIP-Seq Data Analysis: Identification of Protein-DNA Binding Sites with SI Newsbot! Literature Watch 0 12-02-2011 05:51 AM
ChIP-Seq: A fully Bayesian hidden Ising model for ChIP-seq data analysis. Newsbot! Literature Watch 0 09-15-2011 03:10 AM
Free Partek RNA-Seq & ChIP-Seq Data Analysis Workshops mgabrielli@partek.com Events / Conferences 0 04-05-2011 08:28 AM
ChIP-Seq: Computational Analysis of ChIP-seq Data. Newsbot! Literature Watch 0 09-10-2010 03:10 AM

Reply
 
Thread Tools
Old 11-01-2010, 04:41 AM   #1
Bioinfo
Member
 
Location: canada

Join Date: Jul 2010
Posts: 15
Default ChIP Seq data analysis

Hi all
I am just wondering that if anyone knows any statistical analysis tools for comparing output from different ChIP Seq data analysis tools. It could also be useful any recommendations for comparison.
Any suggestions would be gratefully appreciated
Thanks in advance
Bioinfo is offline   Reply With Quote
Old 11-11-2010, 06:26 PM   #2
hwu
Junior Member
 
Location: Atlanta

Join Date: Nov 2010
Posts: 4
Default

What do you want to compare? Most software output a list of peaks. YOu want to know which peak lists give better ranks? Without gold standard it'll be difficult.
hwu is offline   Reply With Quote
Old 11-21-2010, 09:54 AM   #3
Karl Kornacker
Junior Member
 
Location: Ohio, USA

Join Date: Jul 2010
Posts: 2
Default

I have developed R scripts for multiway analysis of multifactor ChIP-seq coverage profiles and invite collaboration to incorporate the scripts into a BioConductor package.
Interested?
Karl Kornacker is offline   Reply With Quote
Old 11-22-2010, 03:29 AM   #4
Bioinfo
Member
 
Location: canada

Join Date: Jul 2010
Posts: 15
Default

Quote:
Originally Posted by Karl Kornacker View Post
I have developed R scripts for multiway analysis of multifactor ChIP-seq coverage profiles and invite collaboration to incorporate the scripts into a BioConductor package.
Interested?
Hi Karl,
Thanks for your help... I would be really grateful if you could share me the scripts.
Kind regards
Bioinfo is offline   Reply With Quote
Old 11-22-2010, 06:13 AM   #5
Karl Kornacker
Junior Member
 
Location: Ohio, USA

Join Date: Jul 2010
Posts: 2
Default

I am preparing a publication on previously unrecognized biologically significant enrichment patterns found by application of a novel multiway data analysis method to a superset of publicly available ChIP-seq datasets. I am inviting pre-publication collaboration, with possible co-authorship.
Karl Kornacker is offline   Reply With Quote
Old 04-01-2014, 06:23 PM   #6
pmad
Bioinformatics Engineer
 
Location: University of Cambridge, UK

Join Date: Jun 2010
Posts: 14
Default

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326. doi:10.1371/journal.pcbi.1003326

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003326
__________________
Pedro Madrigal
pmad 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 12:37 AM.


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