GeneAtlas

DESCRIPTION

GeneAtlas is a 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

  -c --score       Method to compute the score: a) norlog, b) wilson [default].
                   "norlog" is the normalized value of the log-enriched-ratio
                   multiplied by the normalized expression level.
                   "wilson" is the lower bound of Wilson score confidence 
                   interval for a Bernoulli parameter (95% conf.)

  -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