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README.md

@@ -1,4 +1,64 @@
 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
+