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1 parent 9c6ab09 commit 580bfa437bde785aa8a5af11875817a15a010e96 @caballero committed May 2, 2012
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GeneAtlas
=========
-GeneAtlas is simple gene enrichment in normal tissue expression profiles.
+DESCRIPTION
+
+GeneAtlas is simple gene enrichment in normal tissue expression profiles.
+We have a selection of publically available data sets for normal human tissue profiling, all data sets are located in the data/ directory, after gene normalization and quantification, please contact me if you want more details about the data preprocessing.
+Input are a selection of tissues to compare, output is a text file with the
+weigthed gene list [0,1).
+
+USAGE
+
+geneatlas.pl [PARAMETERS]
+
+ Parameters Description
+
+ -d --dataset Select data set to use, "all" shows all data sets available.
+
+ -l --list List samples in data set.
+
+ -s --select Select samples, the value is a list of numbers or the name
+ of the samples, a basic RegEx is applied in text mode.
+ Multiple sources can be separated by commas.
+
+ -e --exclude Exclude samples, similar to "select" option, but it will
+ skip the samples in the computation.
+
+ -m --method Method for enrichment, multiple values are collapsed using:
+ a) maximal [default], b) average
+
+ -t --transcript Report genes at the transcript level (default is collapsing
+ transcripts values to the gene level).
+
+ -o --out Write ouput to this file [default: stdout]
+
+ -h --help Show this screen.
+
+ -v --verbose Activate verbose mode.
+
+ --version Print version and exit.
+
+EXAMPLES
+
+ 1. Show available data sets
+ perl bin/geneatlas.pl -d all
+
+ 2. Show samples in one data set
+ perl bin/geneatlas.pl -d GSE1133 -l
+
+ 3. Compute enrichment in the Appendix in data set GSE1133_microrray
+ perl bin/geneatlas.pl -d GSE1133_microrray -s 7
+ perl bin/geneatlas.pl -d GSE1133_microrray -s Appendix # this also works
+
+ 4. Compute enrichment in the Appendix in data set GSE1133_microrray excluding CD* samples
+ perl bin/geneatlas.pl -d GSE1133_microrray -s 7 -e 10,15,20,29,36,38,43,61,66
+ perl bin/geneatlas.pl -d GSE1133_microrray -s Appendix -e CD # this also works
+
+ 5. Change the method to average values
+ perl bin/geneatlas.pl -d GSE1133_microrray -s 7 -m average
+
+AUTHOR
+
+Juan Caballero, Institute for Systems Biology @ 2012
+

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