Table of Contents

Comparison of Gene Expression Profiles in Non-Model Eukaryotic Organisms with RNA-Seq.- Microarray Data Analysis for Transcriptome Profiling.- Pathway and Network Analysis of Differentially Expressed Genes in Transcriptomes.- QuickRNASeq: Guide for Pipeline Implementation and for Interactive Results Visualization.- Tracking Alternatively Spliced Isoforms from Long Reads by SpliceHunter.- RNA-Seq-Based Transcript Structure Analysis with TrBorderExt.- Analysis of RNA Editing Sites from RNA-Seq Data Using GIREMI.- Bioinformatic Analysis of MicroRNA Sequencing Data.- Microarray-Based MicroRNA Expression Data Analysis with Bioconductor.- Identification and Expression Analysis of Long Intergenic Non-Coding RNAs.- Analysis of RNA-Seq Data Using TEtranscripts.- Computational Analysis of RNA-Protein Interactions via Deep Sequencing.- Predicting Gene Expression Noise from Gene Expression Variations.- A Protocol for Epigenetic Imprinting Analysis with RNA-Seq Data.- Single-Cell Transcriptome Analysis Using SINCERA Pipeline.- Mathematical Modeling and Deconvolution of Molecular Heterogeneity Identifies Novel Subpopulations in Complex Tissues.