Difference between revisions of "GeneXplorer"
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| − | + | GeneXplorer is a web application that allows clustered [[:Category:Microarrays|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. | |
| − | + | == Status == | |
| + | GeneXplorer is still actively supported (see [[#Contact|Contact]] below), but as of January 2009, we are not developing any new features for it. One thing that we may consider in the future is allowing it to use the "extended pcl" file, which allows arbitrary numbers of columns of annotation, as we are trying to do this throughout our microarray infrastructure. | ||
==Demo & Screenshots== | ==Demo & Screenshots== | ||
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[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.] | ||
| + | It has been published in: | ||
| + | |||
| + | [http://www.biomedcentral.com/1471-2105/5/141 Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G. (2004). GeneXplorer: an interactive web application for microarray data visualization and analysis. ''BMC Bioinformatics'' '''5''':141] | ||
==Requirements== | ==Requirements== | ||
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GeneXplorer is written in Perl, and thus requires a system that is capable of running Perl. GeneXplorer also requires the following Perl modules: | 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/Getopt-Long/ Getopt::Long] | |
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.] | 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.] | ||
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]. | 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]. | ||
| − | |||
==Documentation== | ==Documentation== | ||
See the README file at the download site (see below). | See the README file at the download site (see below). | ||
| − | |||
==Contact== | ==Contact== | ||
| − | [ | + | [mailto:sherlock@genome.stanford.edu Gavin Sherlock]. |
| − | + | ||
==Downloads== | ==Downloads== | ||
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GeneXplorer is freely available under the MIT license from [http://search.cpan.org/dist/Microarray-GeneXplorer/ CPAN]. | GeneXplorer is freely available under the MIT license from [http://search.cpan.org/dist/Microarray-GeneXplorer/ CPAN]. | ||
| − | + | [[Category:Expression]] | |
| + | [[Category:Microarrays]] | ||
[[Category:GMOD Components]] | [[Category:GMOD Components]] | ||
Latest revision as of 18:57, 13 July 2012
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.
Status
GeneXplorer is still actively supported (see Contact below), but as of January 2009, we are not developing any new features for it. One thing that we may consider in the future is allowing it to use the "extended pcl" file, which allows arbitrary numbers of columns of annotation, as we are trying to do this throughout our microarray infrastructure.
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:
It has been published in:
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.
