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The Gene Expression Deconvolution Interactive Tool and other data associated with the project
License: Other
This project forked from bnadel/gedit
The Gene Expression Deconvolution Interactive Tool and other data associated with the project
License: Other
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.
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