Normalization package for BASE

This package contains different kinds of normalization plug-ins, each one implementing a specific algorithm.
The plug-ins in this package require BASE 2.7.0 or later.

Normalization algorithms supported in this package:

• Average normalization
• Quantile normalization

More about the plug-ins and their algorithms can be found in the README​ file.

Documentation

Stable release

README​ contains general information about the plug-ins in this package.
INSTALL​ contains installation instructions.

Beta release

README​ contains general information about the plug-ins in this package.
INSTALL​ contains installation instructions.

License

The Normalization package for BASE package is an open source project and is available free of charge under the ​GNU General Public License version 3.

Download

Version	Revision	Date	Binary (tar.gz)	BASE Version*
1.1-beta2	2177	December 12, 2013	normalization-plugins-1.1-beta2.tar.gz​ (MD5​) (165kB)	3.2.4	changelog
1.1-beta	1455	November 3, 2011	normalization-plugins-1.1-beta.tar.gz​ (157kB)	3.0	changelog
1.0	934	December 18, 2008	normalization-plugins-1.0.tar.gz​ (MD5​) (34kB)	2.7	changelog

* In general, each release works with the specified and later BASE versions, except that releases for BASE 2 do not work with BASE 3.

Source code is included in the downloads, but can also retrieved from the subversion repository. Use the following command to get source code for the 1.0 version:

svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.normalizers/tags/1.0 normalizers-1.0

The latest development (maybe unstable; do not use on a production server) revision can be checked out from the repository using the following command:

svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.normalizers/trunk normalizers-dev

Contribute

After making modifications to the source code, compose a clear and concise log message to describe those changes and the reasons for them. Then, send an email to the developers list containing your log message and the output of svn diff (from the top of your subversion working copy). If the community members consider your changes acceptable, someone who has commit privileges will add your changes to the public source code tree. Recall that permission to directly commit changes to the repository is granted on merit - if you demonstrate comprehension of subversion, programming competency, and a team spirit, you will likely be awarded that permission.

Feedback

Please use the ​BASE mailing lists for discussions about the normalization plug-ins. You have to login to this trac environment to be able to report bugs, enhancement ideas, and feature requests. Login with userid base and password base and use the ​ticket reporting system.

TODO

Assigned tickets:

#225

qQuantiler should select all assays as reference by default

#267

Change qQuantilerNormalization underlying binary to use the new BFS format

#268

Refactor qQuantileNormalizer plugin to use the ExternalProgramExecutor plugin

Open but not assigned tickets:

#119

Create rank invariant normalizer

#210

net.sf.basedb.normalizers: Add proper 2-channel support to qQuantileNormalizer

#211

Request: R/G quantile normalization

All open tickets

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