Statistical Methods for Bulk and Single-cell RNA Sequencing Data

Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies on bulk tissues. Recently, the emerging single-cell RNA sequencing (scRNA-seq) technologies enable the investigation of transcriptomic landscapes at a single-cell resolution, providing a chance to characterize stochastic heterogeneity within a cell population. The analysis of bulk and single-cell RNA-seq data at four different levels (samples, genes, transcripts, and exons) involves multiple statistical and computational questions, some of which remain challenging up to date. The first part of this dissertation focuses on the statistical challenges in the transcript-level analysis of bulk RNA-seq data. The next-generation RNA-seq technologies have been widely used to assess full-length RNA isoform structure and abundance in a high-throughput manner, enabling us to better understand the alternative splicing process and transcriptional regulation mechanism. However, accurate isoform identification and quantification from RNA-seq data are challenging due to the information loss in sequencing experiments. In Chapter 2, given the fast accumulation of multiple RNA-seq datasets from the same biological condition, we develop a statistical method, MSIQ, to achieve more accurate isoform quantification by integrating multiple RNA-seq samples under a Bayesian framework. The MSIQ method aims to (1) identify a consistent group of samples with homogeneous quality and (2) improve isoform quantification accuracy by jointly modeling multiple RNA-seq samples and allowing for higher weights on the consistent group. We show that MSIQ provides a consistent estimator of isoform abundance, and we demonstrate the accuracy of MSIQ compared with alternative methods through both simulation and real data studies. In Chapter 3, we introduce a novel method, AIDE, the first approach that directly controls false isoform discoveries by implementing the statistical model selection principle. Solving the isoform discovery problem in a stepwise manner, AIDE prioritizes the annotated isoforms and precisely identifies novel isoforms whose addition significantly improves the explanation of observed RNA-seq reads. Our results demonstrate that AIDE has the highest precision compared to the state-of-the-art methods, and it is able to identify isoforms with biological functions in pathological conditions.The second part of this dissertation discusses two statistical methods to improve scRNA-seq data analysis, which is complicated by the excess missing values, the so-called dropouts due to low amounts of mRNA sequenced within individual cells. In Chapter 5, we introduce scImpute, a statistical method to accurately and robustly impute the dropouts in scRNA-seq data. The scImpute method automatically identifies likely dropouts, and only performs imputation on these values by borrowing information across similar cells. Evaluation based on both simulated and real scRNA-seq data suggests that scImpute is an effective tool to recover transcriptome dynamics masked by dropouts, enhance the clustering of cell subpopulations, and improve the accuracy of differential expression analysis. In Chapter 6, we propose a flexible and robust simulator, scDesign, to optimize the choices of sequencing depth and cell number in designing scRNA-seq experiments, so as to balance the exploration of the depth and breadth of transcriptome information. It is the first statistical framework for researchers to quantitatively assess practical scRNA-seq experimental design in the context of differential gene expression analysis. In addition to experimental design, scDesign also assists computational method development by generating high-quality synthetic scRNA-seq datasets under customized experimental settings