Wikiomics:ChIP-chip - Revision history

Darek Kedra: /* Programs used to analyze ChIP-CHIP data */

Darek Kedra — Thu, 31 Jul 2008 18:04:41 GMT

Programs used to analyze ChIP-CHIP data

←Older revision		Revision as of 18:04, 31 July 2008
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	* [http://transcriptome.affymetrix.com/download/Nix/TiMAT2/ TiMAT2] is a collection of command line java tools used for for both low and high level tiling microarray data analysis using the Affymetrix, Nimblegen, and Agilent platforms. TiMAT2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets. Options exist for distributed computing on a cluster via PBS. (dead link Nov 2007)		* [http://transcriptome.affymetrix.com/download/Nix/TiMAT2/ TiMAT2] is a collection of command line java tools used for for both low and high level tiling microarray data analysis using the Affymetrix, Nimblegen, and Agilent platforms. TiMAT2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets. Options exist for distributed computing on a cluster via PBS. (dead link Nov 2007)

-	* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi TAMALPAIS]: Web-based online analysis of ChIP-chip data (gff format); emails results to user	+	* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi TAMALPAIS]: Web-based online analysis of ChIP-chip data (gff format); emails results to user. Stand alone version available from author.

	* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/promoterarray.cgi Promoter Array Analysis Server]: simple list comparison for NimbleGen summary files for Minimum Promoter Designs; displays in browser		* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/promoterarray.cgi Promoter Array Analysis Server]: simple list comparison for NimbleGen summary files for Minimum Promoter Designs; displays in browser
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	ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.		ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

-	* [http://bdtnp.lbl.gov/TiMAT TiMAT]	+	* [http://bdtnp.lbl.gov/TiMAT TiMAT]
-		+

	== References ==		== References ==

Torsten Waldminghaus: add tag

Torsten Waldminghaus — Wed, 27 Feb 2008 11:23:58 GMT

add tag

←Older revision		Revision as of 11:23, 27 February 2008
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	* [[User:Darked\|Darek Kedra]] wrote this tutorial		* [[User:Darked\|Darek Kedra]] wrote this tutorial
	<!-- other contributors, put yourself here -->		<!-- other contributors, put yourself here -->
		+
		+
		+	[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]]

Darek Kedra: + credits

Darek Kedra — Fri, 23 Nov 2007 21:06:16 GMT

+ credits

←Older revision		Revision as of 21:06, 23 November 2007
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	#DRIM Eden E, Lipson D, Yogev S, Yakhini Z (2007) Discovering Motifs in Ranked Lists of DNA Sequences. PLoS Comput Biol 3(3): e39 doi:10.1371/journal.pcbi.0030039		#DRIM Eden E, Lipson D, Yogev S, Yakhini Z (2007) Discovering Motifs in Ranked Lists of DNA Sequences. PLoS Comput Biol 3(3): e39 doi:10.1371/journal.pcbi.0030039
	</biblio>		</biblio>
		+
		+	== Credits ==
		+
		+	{{credits}}
		+
		+	* [[User:Darked\|Darek Kedra]] wrote this tutorial
		+	<!-- other contributors, put yourself here -->

Darek Kedra: new tools added

Darek Kedra — Fri, 23 Nov 2007 21:05:15 GMT

new tools added

←Older revision		Revision as of 21:05, 23 November 2007
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	* [http://proteus.nimblegen.com/products/software/signalmap.html SignalMap] (Nimblegene) uses gff format; useful mostly for visualization		* [http://proteus.nimblegen.com/products/software/signalmap.html SignalMap] (Nimblegene) uses gff format; useful mostly for visualization

-	* [http://transcriptome.affymetrix.com/download/Nix/TiMAT2/ TiMAT2] is a collection of command line java tools used for for both low and high level tiling microarray data analysis using the Affymetrix, Nimblegen, and Agilent platforms. TiMAT2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets. Options exist for distributed computing on a cluster via PBS.	+	* [http://transcriptome.affymetrix.com/download/Nix/TiMAT2/ TiMAT2] is a collection of command line java tools used for for both low and high level tiling microarray data analysis using the Affymetrix, Nimblegen, and Agilent platforms. TiMAT2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets. Options exist for distributed computing on a cluster via PBS. (dead link Nov 2007)

	* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi TAMALPAIS]: Web-based online analysis of ChIP-chip data (gff format); emails results to user		* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi TAMALPAIS]: Web-based online analysis of ChIP-chip data (gff format); emails results to user
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	* [http://www.stat.ucla.edu/~zmdl/ Mpeak] <cite>mpeak</cite> Win only ver.2 ?not working?		* [http://www.stat.ucla.edu/~zmdl/ Mpeak] <cite>mpeak</cite> Win only ver.2 ?not working?

-	* [http://ceas.cbi.pku.edu.cn/index.html CEAS] BED/GFF file format ([http://genome.ucsc.edu/FAQ/FAQformat#format1 BED format]) so far only human ~~genome?~~	+	* [http://ceas.cbi.pku.edu.cn/index.html CEAS] BED/GFF file format ([http://genome.ucsc.edu/FAQ/FAQformat#format1 BED format]) so far only human and mouse genomes, web based

	* [http://chip.dfci.harvard.edu/~wli/HMM.Tiling/HMMTiling/HMMTiling_Readme.htm HMMTiling]		* [http://chip.dfci.harvard.edu/~wli/HMM.Tiling/HMMTiling/HMMTiling_Readme.htm HMMTiling]
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	* [http://bioinfo.cs.technion.ac.il/drim/ DRIM] online and stand alone program (2007) <cite>DRIM</cite>		* [http://bioinfo.cs.technion.ac.il/drim/ DRIM] online and stand alone program (2007) <cite>DRIM</cite>
		+
		+	* [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1906858 Ringo](R package, 2007)
		+
		+	* [http://bioconductor.org/packages/2.1/bioc/html/ACME.html ACME] (R package),
		+	ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.
		+
		+	* [http://bdtnp.lbl.gov/TiMAT TiMAT]
		+

	== References ==		== References ==

Bill Flanagan: 1 revision(s)

Bill Flanagan — Tue, 20 Nov 2007 04:00:29 GMT

1 revision(s)

←Older revision

Revision as of 04:00, 20 November 2007

Darked: +DRIM

Darked — Fri, 20 Jul 2007 15:03:41 GMT

+DRIM

New page

{{stub}}

Information about the method is here: [[wikipedia:ChIP-on-chip]]

== Programs used to analyze ChIP-CHIP data ==

* [http://proteus.nimblegen.com/products/software/signalmap.html SignalMap] (Nimblegene) uses gff format; useful mostly for visualization

* [http://transcriptome.affymetrix.com/download/Nix/TiMAT2/ TiMAT2] is a collection of command line java tools used for for both low and high level tiling microarray data analysis using the Affymetrix, Nimblegen, and Agilent platforms. TiMAT2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets. Options exist for distributed computing on a cluster via PBS.

* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/tamalpais.cgi TAMALPAIS]: Web-based online analysis of ChIP-chip data (gff format); emails results to user

* [http://chipanalysis.genomecenter.ucdavis.edu/cgi-bin/promoterarray.cgi Promoter Array Analysis Server]: simple list comparison for NimbleGen summary files for Minimum Promoter Designs; displays in browser

* [http://www.bio.unc.edu/faculty/lieb/labpages/ChIPOTle/home.htm ChIPOTle Microsoft Excel]: Microsoft Excel macros. Restriction on maximum number of rows accepted by Excel (ca 64k).

* [http://www.stat.ucla.edu/~zmdl/ Mpeak] <cite>mpeak</cite> Win only ver.2 ?not working?

* [http://ceas.cbi.pku.edu.cn/index.html CEAS] BED/GFF file format ([http://genome.ucsc.edu/FAQ/FAQformat#format1 BED format]) so far only human genome?

* [http://chip.dfci.harvard.edu/~wli/HMM.Tiling/HMMTiling/HMMTiling_Readme.htm HMMTiling]

* [http://biogibbs.stanford.edu/~jihk/TileMap/index.htm TileMap] <cite>tilemap</cite>

* [http://www.stat.wisc.edu/~keles/software.html TileHGMM]: R package, requires replicates from chips, plus probe location file. For computational reasons data sould be separated for each chromosome.

* [http://llama.med.harvard.edu/cgi/Chipper/chip3.py Chipper] online and stand-alone R-based software (2006) <cite>Chipper</cite>

* [http://bioinfo.cs.technion.ac.il/drim/ DRIM] online and stand alone program (2007) <cite>DRIM</cite>

== References ==

<biblio>
#tilemap pmid=16046496
#mpeak Zheng M, Barrera LO, Ren B, and Wu YN. ''ChIP-chip: Data, Model, and Analysis''. University of California, Los Angeles, 2005. [http://scholar.google.com/url?sa=U&q=http://repositories.cdlib.org/cgi/viewcontent.cgi%3Farticle%3D1074%26context%3Duclastat PDF] 

#Chipper pmid=16277751 [http://genomebiology.com/2005/6/11/R96#B30]
#DRIM Eden E, Lipson D, Yogev S, Yakhini Z (2007) Discovering Motifs in Ranked Lists of DNA Sequences. PLoS Comput Biol 3(3): e39 doi:10.1371/journal.pcbi.0030039
</biblio>