README.txt

This repository contains:

GEDITv2.2: The latest version of GEDIT that runs on python2

GEDITv3.0: The latest version of GEDIT that runs on python3

ReferenceMatrices: A set of reference matrices that can be used with the tool when applying to novel data

ExampleMixtures: Two sample mixture matrix files. ImmuneCellMix.tsv is a dataset created in-vitro and published along with the GEDIT paper. SkinDiseases.tsv represents expression data collected from a set of biopsies from various skin conditions, published in a previous study (Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol 2017;18) 220)

To keep the download size small, additional elements have been moved to a separate repository: https://github.com/BNadel/GEDITExpanded. These include previous versions of GEDIT, application examples presented in the paper, and the large ImmGen reference matrix for mouse

GEDIT Publication: Brian B Nadel, David Lopez, Dennis J Montoya, Feiyang Ma, Hannah Waddel, Misha M Khan, Serghei Mangul, Matteo Pellegrini, The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data, GigaScience, Volume 10, Issue 2, February 2021, giab002, https://doi.org/10.1093/gigascience/giab002