flexible tool to search allen brain atlases
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README

ALLENMINER: a tool to find patterns of interest in the Allen Brain Atlas
========================================================================
Version 2.1; Dec 10, 2015.
http://fredpdavis.com/allenminer
Copyright 2008, 2012, 2015  Fred P. Davis


What is ALLENMINER?
-------------------
ALLENMINER searches for genes that express in patterns of interest in the
developing or adult mouse Allen Brain Atlases (ABA).

It can search in any region of interest for genes that:
1. express
2. express specifically
3. express non-uniformly
4. express in a graded fashion
5. express in a pattern similar to a query gene

The region of interest can be specified as a set of brain region names or as
x,y,z bounds of a cuboid region of interest.

The code includes several routines that are generally useful for processing ABA
data files, including parsers for XML and XPZ files. Besides accessing the
raw data, these routines are useful for visualizing ABA expression files on
platforms where the ABA BrainExplorer application is not available (eg,
GNU/Linux). For example, all ABA expression files can be converted to PDB
(protein data bank) format for visualization in protein structure viewers, such
as PyMOL (http://pymol.org).

I began to develop ALLENMINER at the HHMI Janelia Research Campus and continue
to maintain it at NIH/NIAMS.

What's new?
------------
Version 2.1 is compatible with the latest adult (v7) and developing (v6) brain
atlases.


Documentation
-------------
docs/allenminer_user_manual.pdf offers detailed instruction on
installation and usage. This README offers a quick guide to a small
subset of the features.


Citing ALLENMINER
-----------------
A tool for identification of genes expressed in patterns of interest using
the Allen Brain Atlas. Fred P. Davis and Sean R. Eddy.
Bioinformatics 2009. 25(13): 1647-54. doi:10.1093/bioinformatics/btp288


Contact information
-------------------
 Fred P. Davis
 http://fredpdavis.com
 fredpdavis@gmail.com

This file is part of ALLENMINER.

ALLENMINER is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

ALLENMINER is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with ALLENMINER.  If not, see <http://www.gnu.org/licenses/>.

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