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Data Analysis Tools
This section contains computer-based tools
used to analyze microarray experiments data. It
permits individuals to browse existing tools
or to add new tools they have developed
The purpose of this section is both to permit the
exchange of tools and to facilitate discussion of
their use. As such, each tool contains a link at
the bottom through which you can add information
related to your experience.
XML-DBMS:
XML-DBMS is middleware for transferring data between XML documents and relational databases.
It views the XML document as a tree of data-specific objects in which element types are generally
viewed as classes and attributes and PCDATA as properties of those classes. It then uses an
object-relational mapping to map these objects to the database. An XML-based mapping language
is used to define the view and map it to the database.
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J-Express:
A Java implementation of hierachical
clustering, self organized maps, and principal
component analysis, with several different viewing
options and output formats
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Stanford Microarray Analysis Suite:
(requires registration)
Cluster Performs a variety of types of cluster
analysis and other types of processing on large
microarray datasets. Currently includes hierarchical
clustering and self-organizing maps (SOMs).
TreeView Graphically browse results of clustering
and other analyses from Cluster. Supports tree-based
and image based browsing of hierarchical trees.
Multiple output formats for generation of images for
publications.
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BRB ArrayTools Microarray Analysis Package:
(registration required)
Integrated microarray data analysis from
the Molecular Statistics and Bioinformatics Section of the
NCI. This package incorporates a wide range of
visualization and statistical analysis tools. Using Excel as the front
end for menu based analyses, back end computation is performed using
the R statistical language as well as JAVA and Fortran programs.
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Ann Arbor Analysis Tools:
Three pieces of software are available, including the code, free for anyone to use and modify.
1) An Affymetrix specific analysis program that reads ".CEL" files and outputs statistitics.
(In C, we use it under Unix-ish systems so far.) 2) Quantile-normalization algorithms that make
the quantiles of two distributions similar. We use it to normalize microarray data. (In C++).
3) A program that annotates sequence data with information from Unigene, locuslink, etc. (In Java).
Publications using the methods are listed.
The tool may be downloaded here.
The discussion for the tool is here.
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Listing
of analytic and data management tools submitted by users and their
related discussions. |
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