Who is this book for?

The book contains practical and theoretical aspects of computational genomics. Biology and medicine generate more data than ever before. Therefore, we need to educate more people with data analysis skills and understanding of computational genomics. Since computational genomics is interdisciplinary, this book aims to be accessible for biologists, medical scientists, computer scientists and people from other quantitative backgrounds. We wrote this book for the following audiences:

• Biologists and medical scientists who generate the data and are keen on analyzing it themselves.
• Students and researchers who are formally starting to do research on or using computational genomics do not have extensive domain-specific knowledge, but have at least a beginner-level understanding in a quantitative field, for example, math, stats.
• Experienced researchers looking for recipes or quick how-to’s to get started in specific data analysis tasks related to computational genomics.

What will you get out of this?

This resource describes the skills and provides how-to’s that will help readers analyze their own genomics data.

After reading:

• If you are not familiar with R, you will get the basics of R and dive right in to specialized uses of R for computational genomics.
• You will understand genomic intervals and operations on them, such as overlap.
• You will be able to use R and its vast package library to do sequence analysis, such as calculating GC content for given segments of a genome or find transcription factor binding sites.
• You will be familiar with visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization.
• You will be familiar with supervised and unsupervised learning techniques which are important in data modeling and exploratory analysis of high-dimensional data.
• You will be familiar with analysis of different high-throughput sequencing datasets (RNA-seq, ChIP-seq, BS-seq and multi-omics integration) mostly using R-based tools.