RNA Bioinformatics / edited by Ernesto Picardi.

Format:

Book

Contributor:

Picardi, Ernesto, Editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1940-6029 ; 2284

Methods in Molecular Biology, 1940-6029 ; 2284

Language:

English

Subjects (All):

Biochemistry.

Bioinformatics.

Local Subjects:

Biochemistry.

Bioinformatics.

Physical Description:

1 online resource (XIV, 581 pages) : 203 illustrations, 178 illustrations in color.

Edition:

2nd ed. 2021.

Contained In:

Springer Nature eBook

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2021.

System Details:

text file PDF

Summary:

This detailed book aims to provide an overview of novel bioinformatics resources for exploring diverse aspects of RNA biology. This edition focuses on methods dealing with non-coding RNA (miRNAs, circRNAs or lncRNAs), RNA modifications (m6A or RNA editing), single cell RNA-seq and statistical models to handle count data from RNA-seq experiments. The book also includes chapters based on the classical RNA bioinformatics methods, such as those for deciphering secondary and tertiary RNA structures; however, they are revised to take into account deep sequencing data. Finally, chapters describing methods to analyze RNA sequencing data from emerging third generation sequencing technologies that could provide interesting insights into the transcriptional process and its regulation are also included. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that encourages quality results. Comprehensive and up-to-date, RNA Bioinformatics, Second Edition serves as an ideal guide for researchers digging ever-deeper into the depths of the study of RNAs. The chapter 'RNA-Seq Data Analysis in Galaxy' is open access under a CC BY 4.0 license.

Contents:

Advanced Design of Structural RNAs Using RNARedPrint

Modeling and Predicting RNA Three-Dimensional Structures

Motif Discovery from CLIP Experiments

Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS

RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing

Using RNentropy to Detect Significant Variation in Gene Expression across Multiple RNA-Seq or Single Cell RNA-Seq Samples

Statistical Modeling of High Dimensional Counts

QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing

Summarizing RNA-Seq Data or Differentially Expressed Genes Using Gene Set, Network or Pathway Analysis

Computational Analysis of circRNA Expression Data

Differential Expression Analysis of Long Non-Coding RNAs

Micro-RNA Quantification, Target Gene Identification, and Pathway Analysis

In Silico Analysis of MicroRNA Sequencing Data

RNA Editing Detection in HPC Infrastructures

Identification of Genes Post-Transcriptionally Regulated from RNA-Seq: The Case Study of Liver Hepatocellular Carcinoma

Computational Analysis of Single Cell RNA-Seq Data

Normalization of Single-Cell RNA-Seq Data

Dimensionality Reduction of Single-Cell RNA-Seq Data

Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview

RNA-Seq Data Analysis in Galaxy

RAP: A Web Tool for RNA-Seq Data Analysis

iDEP Web Application for RNA-Seq Data Analysis

Exploring Non-Invasive Biomarkers with the miRandola Database: A Tool for Translational Medicine

Database Resources for Functional Circular RNAs

Databases for RNA Editing Collections

MODOMICS: An Operational Guide to the Use of the RNA Modification Pathways Database

MeT-DB V2.0: Elucidating Context-Specific Functions of N6-Methyl-Adenosine Methyltranscriptome

WHISTLE: A Functionally Annotated High-Accuracy Map of Human m6A Epitranscriptome

Transcript Identification through Long-Read Sequencing

Transcript Isoform-Specific Estimation of Poly(A) Tail Length by Nanopore Sequencing of Native RNA

Nanopore RNA Sequencing Analysis.

Other Format:

Printed edition:

ISBN:

978-1-0716-1307-8

9781071613078

Access Restriction:

Restricted for use by site license.