Icbwiki - Recent changes [en]

Elementolab/Social Media

Ole2001 — Mon, 27 May 2013 19:34:53 GMT

Revision as of 19:34, 27 May 2013		Current revision
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	<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";		<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";
	fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>		fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
		+
		+	* NLTK is a great Python library for NLP
		+	http://nltk.org/
		+
		+	An example
		+	http://bommaritollc.com/2011/02/16/pre-processing-text-rtm-vs-pythonnltk/
		+
		+	The book
		+	http://nltk.org/book/

Ole2001 — Mon, 27 May 2013 19:33:02 GMT

Revision as of 19:33, 27 May 2013		Current revision
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	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Big_Data Big Data]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Big_Data Big Data]
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/DataVisualization Data Visualization]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/DataVisualization Data Visualization]
-	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Social_Media Social Media Howtos]	+	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Social_Media Social Media Howtos and Natural Language Processing]

Eug2002 — Thu, 23 May 2013 17:35:07 GMT

/* Files you will need */

Revision as of 17:35, 23 May 2013		Current revision
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	\|-		\|-
	\| zebrafish (zv9)		\| zebrafish (zv9)
-	\| http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/mm9.tar.gz	+	\| http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/zv9.tar.gz
	\|-		\|-
	\| saccharomyces cerevisiae		\| saccharomyces cerevisiae

Ole2001 — Sun, 19 May 2013 15:53:15 GMT

/* Loading mutations into the cBio portal */

Revision as of 15:53, 19 May 2013		Current revision
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-	Login and load data	+	Login and load data:
	ssh -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com		ssh -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com
	cd $PORTAL_HOME/core/src/main/scripts		cd $PORTAL_HOME/core/src/main/scripts
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	sudo /etc/init.d/tomcat6 stop		sudo /etc/init.d/tomcat6 stop
	sudo /etc/init.d/tomcat6 start		sudo /etc/init.d/tomcat6 start
		+
		+	To load CNAs: (data_CNA.txt being matrix of +1, 0, -1 etc for each gene, typically generated by GISTIC)
		+	$PORTAL_HOME/core/src/main/scripts/importProfileData.pl --data $PORTAL_DATA_HOME/studies/baca/data_CNA.txt \
		+	--meta $PORTAL_DATA_HOME/studies/baca/meta_CNA.txt --dbmsAction clobber
		+

Ole2001 — Sat, 11 May 2013 17:57:27 GMT

Revision as of 17:57, 11 May 2013		Current revision
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	* remove adapters		* remove adapters

-	If the adapters have been masked:	+	If the adapters have been masked, eg by the core:

	for f in s_*.txt.gz; do gr_5n "perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/fastq_remove_N_adapters.pl $f" --name=rem$f; done		for f in s_*.txt.gz; do gr_5n "perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/fastq_remove_N_adapters.pl $f" --name=rem$f; done
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	Otherwise use Smith-Waterman:		Otherwise use Smith-Waterman:

-	for f in *.gz; do echo $f; gr_5n "/home/ole2001/PROGRAMS/SMITH-WATER/remove_miRNA_adapter $f \| gzip > $f.noadapt.gz" -name S$f ; done	+	for f in *.gz; do echo $f; gr_5n "/home/ole2001/PROGRAMS/SMITH-WATER/remove_miRNA_adapter -fastqfile $f \| gzip > $f.noadapt.gz" -name S$f ; done


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	perl /home/ole2001/PROGRAMS/miRSeeqer/run_miRSeeqer.pl --samples=samples_info.txt --mir=1 --genome=hg19		perl /home/ole2001/PROGRAMS/miRSeeqer/run_miRSeeqer.pl --samples=samples_info.txt --mir=1 --genome=hg19
		+
		+
		+	* run stats analysis
		+
		+	perl ~/PROGRAMS/miRSeeqer/run_miRSeeqer_summarize_stats.pl --samples=sample_infos.txt

Tas2019 — Fri, 10 May 2013 01:47:25 GMT

/* Generate random mappable regions */

Revision as of 01:47, 10 May 2013		Current revision
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	--norm Mappability track contains normalized scores		--norm Mappability track contains normalized scores
	--block Output randomly selected regions as <res> bp blocks		--block Output randomly selected regions as <res> bp blocks
		+
		+	E.g. This command generates 500 10kb regions with mappability > 0.9. The mappability file is in bed format and contains the mappability score for all 10kb windows in the genome.
		+	./geneModel util -cmd gen-map -i data/mappability_50bp_chr_10K.txt -res 10000 -n 500 --norm -min 0.9

	===Perform Fisher's exact tests===		===Perform Fisher's exact tests===