Transcriptome Data Analysis

An RNA-Seq Data Analysis Pipeline.- Inferring Interaction Networks from Transcriptomic Data: Methods and Applications.- EMPathways2: Estimation of Enzyme Expression and Metabolic Pathway Activity Using RNA-Seq Reads.- Efficient and Powerful Integration of Targeted Metabolomics and Transcriptomics for Analyzing the Metabolism Behind Desirable Traits in Plants.- A RNAseq Data Analysis for Differential Gene Expression Using HISAT2-stringTie-Ballgown Pipeline.- RNA-Sequencing Experimental Analysis Workflow Using Caenorhabditis elegans.- Inferring Novel Cells in Single Cell RNA Sequencing Data.- Unsupervised Single-Cell Clustering with Asymmetric Within-Sample Transformation and Per Cluster Supervised Features Selection.- Inferring Tree-Shaped Single-Cell Trajectories with Totem.- Zebrafish Thrombocyte Transcriptome Analysis and Functional Genomics.- Plant Transcriptome Analysis with HISAT-StringTie-Ballgown and TopHat-Cufflinks Pipelines.- Cotton Meristem Transcriptomes: Constructing an RNA-Seq Pipeline to Explore Crop Architecture Regulation.- Detecting Somatic Insertions/Deletions (Indels) Using Tumor RNA-Seq Data.- A Protocol for the Detection of Fusion Transcripts Using RNA-Sequencing Data.- GAN Learning Methods for Bulk RNA-Seq Data and Their Interpretive Application in the Context of Disease Progression.- Protocol for Analyzing Epigenetic Regulation Mechanisms in Breast Cancer.- Identification of Virus-Derived Small Interfering RNAs (vsiRNAs) from Infected sRNA-Seq Samples.- Incorporating Sequence-Dependent DNA Shape and Dynamics into Transcriptome Data Analysis.- Utilizing RNA-Seq Data to Infer Bacterial Transcription Termination Sites and Validate Predictions.- RNA-Seq Analysis of Mammalian Prion Disease.- In Silico Identification of tRNA Fragments, Novel Candidates for Cancer Biomarkers, and Therapeutic Targets.