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Source code used in the preparation of my dissertation, including the SOPHIA and EPISTEME algorithms, the SOPHIA workflow, the prior cohort analysis code for data import into EPISTEME

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umut-h-toprak/PhD_Dissertation_codebase

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Code repository for the dissertation titled "Integrative Analysis of Omics Datasets", Umut Toprak, 30.07.2019

This code repository covers the generation methods of presented data in the thesis, whereever possible.

Chapter 1 is excluded from this repository because the results were obtained either by manual inspections in IGV or by interactive analysis in R2. Chapter 2, SOPHIA uses code from the sub-repositories 01, 02, 03 and 04 Chapter 3, EPISTEME uses code from the sub-repositories 05, 06 and 07 Chapter 4 used various features of EPISTEME

In each sub-repository, there are individual README files describing the aims and functions of the code therein.

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Source code used in the preparation of my dissertation, including the SOPHIA and EPISTEME algorithms, the SOPHIA workflow, the prior cohort analysis code for data import into EPISTEME

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