tejasvene / gedit Goto Github PK

Author: Brian Nadel


The data and scripts here represent the 

Contents are as follows

Application:
	As detailed in the GEDIT paper, we have applied GEDIT to tissue samples taken in vivo in 3 contexts.
        These are a) the GTEX database b) the mouse body atlas and c) a set of skin samples from humans with various skin diseases


GEDITv1.6:
	This contains a previous version of GEDIT, which runs preprocessing steps in python and the final linear regression in R
	
GEDITv2.0
	This most recent version of GEDIT is streamlined to be run entirely in python2

ReferenceMatrices:
        We have obtained or assembled 11 references matrices that are saved here and available for use by other parties

Synthetic Mixtures and Parameter Evaluation:
	As detailed in figure 2 of the GEDIT manuscript, and in the supplementary materials,
        the development of GEDIT involved the generation of 10,000 simulated mixtures that were used to tune several parameter settings.

ToolsComparison:
	This directory contains the scripts and data to run 4 deconvolution tools on 3 mixtures of known proportions.
 	We did this with 4 possible choices of reference matrices in each case, and compared the quality of predictions.