ChIP Seq data analysis

Bioinfo · 11-01-2010, 04:41 AM

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

hwu · 11-11-2010, 06:26 PM

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.

Karl Kornacker · 11-21-2010, 09:54 AM

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?

Bioinfo · 11-22-2010, 03:29 AM

Quote:

Originally Posted by Karl Kornacker

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

Karl Kornacker · 11-22-2010, 06:13 AM

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.

pmad · 04-01-2014, 06:23 PM

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

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11-01-2010, 04:41 AM	#1
Bioinfo Member Location: canada Join Date: Jul 2010 Posts: 15	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

04-01-2014, 06:23 PM	#6
pmad Bioinformatics Engineer Location: University of Cambridge, UK Join Date: Jun 2010 Posts: 14	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

11-11-2010, 06:26 PM	#2
hwu Junior Member Location: Atlanta Join Date: Nov 2010 Posts: 4	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.

11-21-2010, 09:54 AM	#3
Karl Kornacker Junior Member Location: Ohio, USA Join Date: Jul 2010 Posts: 2	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?

11-22-2010, 06:13 AM	#5
Karl Kornacker Junior Member Location: Ohio, USA Join Date: Jul 2010 Posts: 2	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.