Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing cellular heterogeneity in biological samples. Various scRNA-seq protocols have been developed that can measure the transcriptome from thousands of cells in a single experiment. With these methods readily available, the ability to transform raw data into biological understanding of complex systems is now a rate-limiting step. In this dissertation, I introduce novel computational software and tools which enhance preprocessing and clustering of scRNA-seq data and evaluate their performance compared to existing methods.
First, I present scruff, an R/Bioconductor package that preprocesses data generated from scRNA-seq protocols including CEL-Seq or CEL-Seq2 and reports comprehensive data quality metrics and visualizations. scruff rapidly demultiplexes, aligns, and counts the reads mapped to genomic features with deduplication of unique molecular identifier (UMI) tags and provides novel and extensive functions to visualize both pre- and post-alignment data quality metrics for cells from multiple experiments.
Second, I present Celda, a novel Bayesian hierarchical model that can perform simultaneous co-clustering of genes into transcriptional modules and cells into subpopulations for scRNA-seq data. Celda identified novel cell subpopulations in a publicly available peripheral blood mononuclear cell (PBMC) dataset and outperformed a PCA-based approach for gene clustering on simulated data.
Third, I extend the application of Celda by developing a multimodal clustering method that utilizes both mRNA and protein expression information generated from single-cell sequencing datasets with multiple modalities, and demonstrate that Celda multimodal clustering captured meaningful biological patterns which are missed by transcriptome- or protein-only clustering methods.
Collectively, this work addresses limitations present in the computational analyses of scRNA-seq data by providing novel methods and solutions that enhance scRNA-seq data preprocessing and clustering.
| Identifer | oai:union.ndltd.org:bu.edu/oai:open.bu.edu:2144/43145 |
| Date | 04 October 2021 |
| Creators | Wang, Zhe |
| Contributors | Campbell, Joshua D., Johnson, W. Evan |
| Source Sets | Boston University |
| Language | en_US |
| Detected Language | English |
| Type | Thesis/Dissertation |
| Rights | Attribution-NonCommercial-ShareAlike 4.0 International, http://creativecommons.org/licenses/by-nc-sa/4.0/ |
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