PICNIC

PICNIC (Predicting Integral Copy Numbers In Cancer) is an algorithm designed to identify copy number segments and genotypes in cancer using a SNP6 'cel' file as input.

All PICNIC code has been made available under a BSD license and shall continue to be developed under this agreement. This code requires Matlab. To use the algorithm without Matlab, use PICNIC_GUI_FULL. To just normalize a .CEL file, use PICNIC_GUI_SHORT.

PICNIC has now been updated to cater for primary tissues that contain normal contamination in addition to cell lines.

[Genome Research Limited]

  • View SNP6 analysis - SNP array based LOH and copy number analysis
    *** Links to CGI that pulls in a lot of data. http://www.sanger.ac.uk/cgi-bin/genetics/CGP/cghviewer/CghViewer.cgi ***
  • Algorithm description - Genome-wide human SNP array 6.0 analysis
    *** Links to another whole page of data. Maybe use tabs, or make an extra page like cnv? http://www.sanger.ac.uk/genetics/CGP/CopyNumberMapping/Affy_SNP6.shtml ***

Downloads

Download Description
PICNIC README file
PICNIC_GUI_FULL README file
PICNIC_GUI_SHORT README file
PICNIC download Public domain ftp repository
PICNIC_GUI_FULL download Public domain ftp repository
PICNIC_GUI_SHORT download Public domain ftp repository
   
figViewer README file
figViewer download (unix) Public domain ftp repository
figViewer download (windows) Public domain ftp repository
   
PICNIC_Primaries README file
PICNIC_Primaries Matlab Version (ftp download)
PICNIC_Primaries Matlab Version (ftp download)

CGP Software License

Copyright © 2006 Genome Research Ltd.
Author: Cancer Genome Project, cgpit@sanger.ac.uk

This software is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software.

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License.

Any redistribution or derivation in whole or in part including any substantial portion of this code must include this copyright and permission notice.

* quick link - http://q.sanger.ac.uk/689qj5zn