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36808.pdf (5.31 MB)
ETD Abstract Container
Abstract Header
Shiny Application for Enrichment and Topological Pathway Analysis
Author Info
Biesiada, Jacek
Permalink:
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595846446399689
Abstract Details
Year and Degree
2020, MS, University of Cincinnati, Medicine: Biostatistics (Environmental Health).
Abstract
EApp (Enrichment Application) Shiny application was developed to facilitate gene enrichment and topological pathway analysis of omics data by scientists without coding skills to support basic biological questions about biological processes and at the same time give people without coding skills the ability to perform those analyses. The application accommodates various external sources of data such as eset with expression and genes signature data, iLINCS project data, GRAIN project data, and raw data (separate data frames with rpkms, count data, and phenotypic data necessary for creating gene signatures). Shiny application provides the user with a graphical user interface that selects appropriate methods based on the source of data and calculated benchmarks. The case study included in thesis were based on TCGA data, and the benchmarks performed in the thesis provide guidelines for using set-based and network-based enrichment methods implemented in the web server.
Committee
Mario Medvedovic, Ph.D. (Committee Chair)
Jaroslaw Meller, Ph.D. (Committee Member)
Pages
52 p.
Subject Headings
Biostatistics
Keywords
Enrichment analysis
;
Pathway analysis
;
Shiny application
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Citations
Biesiada, J. (2020).
Shiny Application for Enrichment and Topological Pathway Analysis
[Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595846446399689
APA Style (7th edition)
Biesiada, Jacek.
Shiny Application for Enrichment and Topological Pathway Analysis.
2020. University of Cincinnati, Master's thesis.
OhioLINK Electronic Theses and Dissertations Center
, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595846446399689.
MLA Style (8th edition)
Biesiada, Jacek. "Shiny Application for Enrichment and Topological Pathway Analysis." Master's thesis, University of Cincinnati, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595846446399689
Chicago Manual of Style (17th edition)
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Document number:
ucin1595846446399689
Download Count:
396
Copyright Info
© 2020, some rights reserved.
Shiny Application for Enrichment and Topological Pathway Analysis by Jacek Biesiada is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by University of Cincinnati and OhioLINK.