Difference between revisions of "GeneXplorer"
From GMOD
(New page: ; '''Description'''<br /> : GeneXplorer is a web application that allows clustered microarray<br /> data to be browsed interactively via the web, and can be used either<br /> for resear...) |
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| + | ==Description== | ||
| + | GeneXplorer is a web application that allows clustered microarray data to be browsed interactively via the web, and can be used either for research purposes, or for providing web supplements to accompany microarray publication. | ||
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| − | + | ==Demo & Screenshots== | |
| − | + | GeneXplorer has been used to provide several web supplements for papers arising from data in the Stanford Microarray Database. As an example, see: | |
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| − | GeneXplorer has been used to provide several web supplements for | + | |
[http://microarray-pubs.stanford.edu/cgi-bin/gx?n=prostate1&rx=5 J Lapointe, C Li, JP Higgins, M van de Rijn, E Bair, K Montgomery, M Ferrari, L Egevad, W Rayford, U Bergerheim, et al: Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A 2004, 101:811-6.] | [http://microarray-pubs.stanford.edu/cgi-bin/gx?n=prostate1&rx=5 J Lapointe, C Li, JP Higgins, M van de Rijn, E Bair, K Montgomery, M Ferrari, L Egevad, W Rayford, U Bergerheim, et al: Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A 2004, 101:811-6.] | ||
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| − | GeneXplorer is written in Perl, and thus requires a system that is | + | ==Requirements== |
| + | |||
| + | GeneXplorer is written in Perl, and thus requires a system that is capable of running Perl. GeneXplorer also requires the following Perl modules: | ||
# [http://search.cpan.org/dist/GD/ GD] | # [http://search.cpan.org/dist/GD/ GD] | ||
# [http://search.cpan.org/dist/Getopt-Long/ Getopt::Long] | # [http://search.cpan.org/dist/Getopt-Long/ Getopt::Long] | ||
| − | In addition, GeneXplorer requires the C-program, correlations, which | + | In addition, GeneXplorer requires the C-program, correlations, which is included in the distribution. This must be compiled with an ANSI compatible compiler, such as [http://gcc.gnu.org/ gcc.] |
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| + | The Clustered datafiles must be created using a clustering program that produces files in the [http://smd.stanford.edu/help/formats.shtml#cdt cdt format]. Such software includes Mike Eisen's [http://rana.lbl.gov/EisenSoftware.htm Cluster], or [http://genetics.stanford.edu/~sherlock/cluster.html XCluster]. | ||
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| + | ==Documentation== | ||
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| + | See the README file at the download site (see below). | ||
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| + | ==Contact== | ||
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| + | [[Gavin Sherlock]]. | ||
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| − | + | ==Downloads== | |
| − | + | GeneXplorer is freely available under the MIT license from [http://search.cpan.org/dist/Microarray-GeneXplorer/ CPAN]. | |
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| − | + | [[Category:GMOD Components]] | |
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Revision as of 17:41, 11 February 2007
Description
GeneXplorer is a web application that allows clustered microarray data to be browsed interactively via the web, and can be used either for research purposes, or for providing web supplements to accompany microarray publication.
Demo & Screenshots
GeneXplorer has been used to provide several web supplements for papers arising from data in the Stanford Microarray Database. As an example, see:
Requirements
GeneXplorer is written in Perl, and thus requires a system that is capable of running Perl. GeneXplorer also requires the following Perl modules:
In addition, GeneXplorer requires the C-program, correlations, which is included in the distribution. This must be compiled with an ANSI compatible compiler, such as gcc.
The Clustered datafiles must be created using a clustering program that produces files in the cdt format. Such software includes Mike Eisen's Cluster, or XCluster.
Documentation
See the README file at the download site (see below).
Contact
Downloads
GeneXplorer is freely available under the MIT license from CPAN.
