Transcriptome Data Analysis

Part I: General Protocols on Transcriptome Data Analysis 1. Comparison of Gene Expression Profiles in Non-Model Eukaryotic Organisms with RNA-Seq Han Cheng, Yejun Wang, and Ming-an Sun 2. Microarray Data Analysis for Transcriptome Profiling Ming-an Sun, Xiaojian Shao, and Yejun Wang 3. Pathway and Network Analysis of Differentially Expressed Genes in Transcriptomes Qianli Huang, Ming-an Sun, and Ping Yan 4. QuickRNASeq: Guide for Pipeline Implementation and for Interactive Results Visualization Wen He, Shanrong Zhao, Chi Zhang, Michael S. Vincent, and Baohong Zhang Part II: Objective-Specialized Transcriptome Data Analysis 5. Tracking Alternatively Spliced Isoforms from Long Reads by SpliceHunter Zheng Kuang and Stefan Canzar 6. RNA-Seq-Based Transcript Structure Analysis with TrBorderExt Yejun Wang, Ming-an Sun, and Aaron P. White 7. Analysis of RNA Editing Sites from RNA-Seq Data Using GIREMI Qing Zhang 8. Bioinformatic Analysis of MicroRNA Sequencing Data Xiaonan Fu and Daoyuan Dong 9. Microarray-Based MicroRNA Expression Data Analysis with Bioconductor Emilio Mastriani, Rihong Zhai, and Songling Zhu 10. Identification and Expression Analysis of Long Intergenic Non-Coding RNAs Ming-an Sun, Rihong Zhai, Qing Zhang, and Yejun Wang 11. Analysis of RNA-Seq Data Using TEtranscripts Ying Jin and Molly Hammell Part III: New Applications of Transcriptome 12. Computational Analysis of RNA-Protein Interactions via Deep Sequencing Lei Li, Konrad U. Forstner, and Yanjie Chao 13. Predicting Gene Expression Noise from Gene Expression Variations Xiaojian Shao and Ming-an Sun 14. A Protocol for Epigenetic Imprinting Analysis with RNA-Seq Data Jinfeng Zou, Daoquan Xiang, Raju Datla, and Edwin Wang 15. Single-Cell Transcriptome Analysis Using SINCERA Pipeline Minzhe Guo and Yan Xu 16. Mathematical Modeling and Deconvolution of Molecular Heterogeneity Identifies Novel Subpopulations in Complex Tissues Niya Wang, Lulu Chen, and Yue Wang