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CITESEQC:A TOOL FOR THE QUALITY CONTROL OF SINGLE CELL RNA-SEQ AND EPITOPE SEQUENCE DATA

Johnson, Maleah (2023) CITESEQC:A TOOL FOR THE QUALITY CONTROL OF SINGLE CELL RNA-SEQ AND EPITOPE SEQUENCE DATA. Master's Thesis, University of Pittsburgh. (Unpublished)

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Abstract

The field of single-cell genomics has proven to be invaluable in investigating complex cell populations. Although data at the single-cell resolution has been revolutionary to genomic research, measuring the transcriptome alone does not provide any information on genotype to phenotype associations. However, quantitatively measuring both the transcriptome inside a cell and the protein markers expressed on its surface, a wet-lab technique called CITE-seq, may bridge this gap. To make sense of this high-dimension multimodal data, researchers must be confident in the quality of the data. Currently, there are no free, single-source bioinformatic tools available dedicated to the quality control of CITE-seq data. The citeseQC R package aims to be the first tool developed with the singular goal of assessing quality of multimodal data. The package is built in a low-code environment making it accessible to users with little to no programming aptitude. The package takes a file directory pathway as input and transforms the CITE-seq out files into interpretable figures to investigate the data quality in markdown report format. It utilizes the power of the Seurat v4.0 package inside its custom functions while retaining an approachable user interface. This paper discusses the current state of the citeseQC package, desired functionality for future version releases, barriers encountered, and successes achieved during its build.

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Details

Item Type: University of Pittsburgh ETD
Status: Unpublished
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Johnson, Maleahmeb301@pitt.edumeb301
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee MemberJung, Hyunhyp15@pitt.eduhyp15
Committee MemberManna, Samanthaslr61@pitt.eduslr61
Thesis AdvisorMinster, Ryan Leerminster@pitt.eduRMINSTER
Date: 3 January 2023
Date Type: Publication
Defense Date: 5 December 2022
Approval Date: 3 January 2023
Submission Date: 16 December 2022
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 47
Institution: University of Pittsburgh
Schools and Programs: School of Public Health > Human Genetics
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: CITE-seq, multimodal quality control, R package
Date Deposited: 03 Jan 2023 13:40
Last Modified: 03 Jan 2023 13:40
URI: http://d-scholarship.pitt.edu/id/eprint/44043

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