Genome Analysis in R

About this book

In recent years the amount of biological sequence data available for research has increased significantly and complete genome sequences have become commonplace. Next-generation sequencing (NGS) is expected to revolutionize biomedical research. However, the analysis of millions of DNA/RNA sequences is becoming a real challenge as the capabilities of standard computers have been far exceeded. Genome Analysis in R guides readers in the processing and analyzing of genome-wide data with minimum computer RAM requirements. It focuses on practical solutions to a wide range of next-generation sequencing bioinformatic problems such as data import, read demultiplexing, trimming, quality checks, alignment, transformations, normalization, annotation, motif search, and differential expression. No prior programming knowledge is required.

Contents

- Preface
- Introduction to Genome Biology
- R Essentials
- Bioconductor Bioinformatics Packages
- Sequence Manipulations
- Parsing Genomic Features
- Next Gen Sequence Processing
- Working with Genomic Databases
- Motif Discovery Packages
- Genome Methylation Analysis
- Transcriptome Analysis (RNA-seq)
- Case studies

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