CAPweb ( Copy number Array analysis Platform on the web ).
A web-based platform for copy number array management and analysis

Version: 2.4
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CAPweb is a web tool devoted to the analysis of copy number microarray data.
CAPweb starts from image analysis results (a gpr file for example) and goes up to biological results.
Different formats are supported by CAPweb:
MAIA -  GENEPIX -  SPOT -  IMAGENE -  AGILENT -  Affymetrix SNP 100k/500k -  Nimblegen Whole Tiling Array.

STEP 1 Upload in a secure mode the results
of your copy number microarray image analysis
(and the annotation of the clones/probes from your array).
First Register !
STEP 2 Automatic normalization of the data.
CAPweb uses the MANOR package,
an algorithm based on a spatial trend computation
by two-dimensional LOESS and unsupervised classification
with spatial contraint.
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STEP 3 Breakpoint detection and status assignment
(gain, loss, normal, amplicon) using the GLAD package.
STEP 4 Validation or deletion of your analysis
based on a synoptic summary report and quality criteria.
STEP 5 Integration within VAMP, a graphical interface
for Visualisation and Analysis of CGH arrays,
transcriptome and other Molecular Profiles.

PHP, Perl, mySQL, Java, Apache and R are used for web service, analysis and file management.
PHP Perl MySQL Java apache R

Have a look at the CAPweb tutorial
For any questions, support, please contact

For a local installation (only for academic), please fill in the license here to receive the CAPweb software.
For commercial use, please contact

Reference: Liva et al;"CAPweb: a bioinformatics CGH array Analysis Platform", Nucleic Acids Research 2006 34(Web Server issue):W477-W481; doi:10.1093/nar/gkl215.
More References, here

- W3C compatible.
- add new format Nimblegen Whole Tiling Genome.

- add new format AFFYMETRIX SNP 100K and 500K.
- new interface.

- add field SIZE for the genome annotation file for the GPR format (to apply some VAMP functionnality).

- add tag ORGANISM (Human and Mouse).

- new project interface.
- new interface for a Patient Number Management.
- import of clinical data.
- import of transcriptome data.
- associate a patient number to an existing analyzed CGH array.

- add a new flag UNIQUE (users can choose to keep or discard the unique spot)
- delete one or several arrays in the array management page.

Contact : capweb support | Bioinformatics Home Page : | Institut Curie Home Page :