بیوانفورماتیک آر ان ای RNA RNA Bioinformatics

فهرست مطالب:

 

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

1 Advanced Design of Structural RNAs Using RNARedPrint . . . . . . . . . . . . . . . . . . 1

2 Modeling and Predicting RNA Three-Dimensional Structures. . . . . . . . . . . . . . . . 17

3 Motif Discovery from CLIP Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

4 Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS . . . . . . . .  . . . 51

5 RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing. . . . . 63

6 Using RNentropy to Detect Significant Variation in Gene Expression Across Multiple RNA-Seq or Single-Cell RNA-Seq Samples. . . . . . . . . . . . . . . . . . 77

7 Statistical Modeling of High Dimensional Counts . . . . . . . . . . . . . . . . . . . . . . . . . . 97

8 QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing . . . . . . . 135

9 Summarizing RNA-Seq Data or Differentially Expressed Genes

Using Gene Set, Network, or Pathway Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

10 Computational Analysis of circRNA Expression Data. . . . . . . . . . . . . . . . . . . . . . . . 181

11 Differential Expression Analysis of Long Noncoding RNAs . . . . . . . . . . . . . . . . . . 193

12 Micro-RNA Quantification, Target Gene Identification,

and Pathway Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207

13 In Silico Analysis of Micro-RNA Sequencing Data . . . . . . . . . . . . . . . . . . . . . . . . . . 231

14 RNA Editing Detection in HPC Infrastructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253

15 Identification of Genes Post-Transcriptionally Regulated from RNA-seq:

The Case Study of Liver Hepatocellular Carcinoma . . . . . . . . . . . . . . . . . . . . . . . . . 271

16 Computational Analysis of Single-Cell RNA-Seq Data. . . . . . . . . . . . . . . . . . . . . . . 289

17 Normalization of Single-Cell RNA-Seq Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303

18 Dimensionality Reduction of Single-Cell RNA-Seq Data . . . . . . . . . . . . . . . . . . . . 331

19 Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview . . . . . . . . . . . . . 343

20 RNA-Seq Data Analysis in Galaxy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367

21 RAP: A Web Tool for RNA-Seq Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393

22 iDEP Web Application for RNA-Seq Data Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . 417

23 Exploring Noninvasive Biomarkers with the miRandola Database:

A Tool for Translational Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445

24 Database Resources for Functional Circular RNAs . . . . . . . . . . . . . . . . . . . . . . . . . . 457

25 Databases for RNA Editing Collections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467

26 MODOMICS: An Operational Guide to the Use of the RNA Modification

Pathways Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481

27 MeT-DB V2.0: Elucidating Context-Specific Functions

of N6-Methyl-Adenosine Methyltranscriptome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507

28 WHISTLE: A Functionally Annotated High-Accuracy Map

of Human m6A Epitranscriptome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 519

29 Transcript Identification Through Long-Read Sequencing . . . . . . . . . . . . . . . . . . . 531

30 Transcript Isoform-Specific Estimation of Poly(A) Tail Length

by Nanopore Sequencing of Native RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 543

31 Nanopore RNA Sequencing Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 569

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579

مشخصات فایل
عنوان (Title):	بیوانفورماتیک آر ان ای RNA RNA Bioinformatics
نام فایل (File name):	591-www.GeneProtocols.ir-RNA Bioinformatics-Humana (2021).pdf
ایجاد کننده:	Ernesto Picardi
زبان (Language):	انگلیسی English
سال انتشار:	2021
شابک ISBN:	1071613065,9781071613061
نوع سند (Doc. type):	کتاب
فرمت (File extention):	pdf
حجم فایل (File size):	37.7 Mb
تعداد صفحات (Book length in pages):	576