File	Date	Author	Commit
DEAP	2014-08-12	Winn Haynes	[a7f019] Labelled classes for unpaired data
RDEAP	2014-08-12	Winn Haynes	[a7f019] Labelled classes for unpaired data
doc	2014-06-18	Winn Haynes	[f0c8de] Run DEAP from any directory (updated rotate.R p...
example	2014-08-12	Winn Haynes	[63bc1a] Labelled classes for unpaired data
pantherParser	2014-05-31	Winn Haynes	[836791] Added PANTHER parser. Corrected rotate.R path
simulateData	2013-06-13	Winn Haynes	[f6f433] Updated contact e-mail
.gitignore	2014-06-18	Winn Haynes	[2fefc2] Removed extra log generation
README.txt	2014-06-18	Winn Haynes	[d6efc5] R wrapper implementation
annotatedExample.pdf	2014-06-18	Winn Haynes	[f0c8de] Run DEAP from any directory (updated rotate.R p...

Read Me

"""
This file is part of DEAP.

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

DEAP 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 Lesser General Public License for more details.

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

This file was written by Winston Haynes. If you have any questions, 
please contact me at: hayneswa@stanford.edu
"""
**********************************
Dependencies: 
   RPy2 (http://rpy.sourceforge.net/)
   		can be installed as pip install rpy2
   Program built on Python 2.7.3
**********************************

*************************
DEAP
	DEAP stands for Differential Expression Analysis for Pathways. DEAP is an approach targeted towards identifying pathways exhibiting significant patterns of differential expression, defined as high differential expression along a subpath of a pathway. 
	If you use this tool, please cite:
		Haynes, et al. Differential Expression Analysis for Pathways. PLoS Computational Biology, 2013.
	For more information, please read the manuscript at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967
*************************

DEAP analysis
	annotatedExample.pdf walks through the python implementation of DEAP.

	RDEAP/sampleExecution.R walks through a sample execution of DEAP using R.

	The 'DEAP/' directory contains all scripts necessary to run a DEAP analysis. Run 'python DEAP.py' from the command line to get proper formatting. DEAP.py takes as input in *.edg files and expression data in *.tsv files, formatted as follows:
	*.edg: Used to represent pathways. A series of lines, where each line represents a single edge and is formatted as follows:
		[Tab delimited reactant names]::[Tab delimited product names]::[True/False- This relationship is catalytic]
		For example, a catalytic edge from P1 to P2 would be represented as 'P1::P2::True'
	*.tsv: Used to represent expression data. A series of lane where the first tab is the identifier of the product being expressed and all other tabs are expression values for that product. Data may be either paired or unpaired. For paired data, it is assumed that the file contains ratios. For unpaired data, it is assumed that the first half of the expression values are for one condition and the second half of the expression values represent the second condition.
		For example, if P1 had two paired samples with expression ratios of 1.3 and 1.5 it would be represented as 'P1\t1.2\t1.5'
		If P2 had two unpaired samples with expression values of 1.1 and 1.2 for condition A and 1.4 and 1.5 for condition B, then it would be represented as 'P2\t1.1\t1.2\t1.4\t1.5'

======================================
Rotation
	'DEAP/rotate.r' provides all scripts necessary to perform rotations. See 'DEAP/deapHelpers.py' for an implementation which calls the rotation usiny RPy2

======================================
Simulation
	'SimulateData/' contains all the scripts necessary to simulate data (as seen in DEAP Validation 1 and 2 in the manuscript). Please read in-script documentation for further details.

=======================================

Parse PANTHER pathway files
	'pantherParser/' contains all the scripts which were used to parse files downloaded from the PANTHER pathway database into the *.edg format.