GitHub - jingchunzhu/cgData: Python API to work with the cgData standard

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Python API to work with the cgData standard

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Name		Name	Last commit message	Last commit date
Latest commit History 218 Commits
CGData		CGData
Rscripts		Rscripts
cgManage		cgManage
examples		examples
scripts		scripts
tests		tests
.gitignore		.gitignore
README		README
raDb.sql		raDb.sql
setup.py		setup.py

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cgData - Cancer Genome Browser Input/Output tools


This python module is designed to do tasks associated with data preperation
associated with Genome/Clinical files to be added to the Cancer Genome Browser
http://genome-cancer.ucsc.edu


===Most of these tools are still in developement===

Tools:

compileCancerData.py - Take collection of data and produce SQL for cancer genome browser
compileScan.py - Do checks on avalible data (doesn't produce actual SQL)

bed2probeMap.py	- Convert bed12 probe file to probeMap format	
	
	
getRefGene_hg18.sh - Download refgene program from Genome Browser database

extractFeatures.py, extractProbes.py, extractGenomic.py, extractSamples.py, extractClinical.py - 
	Extract data stored in previous mySQL schema ( to help with transition to cgData 1.0 )


tcgaAliquotSampleMap.sh - Produce sample map from TCGA sample report