NGS Analysis Basics

Author: Thomas Girke

Last update: 30 April, 2016

Alternative formats of this vignette: Single-page .Rmd HTML, .Rmd, .R Old Slides .pdf

Overview

Sequence Analysis in R and Bioconductor

R Base

• Some basic string handling utilities. Wide spectrum of numeric data analysis tools.

Bioconductor

Bioconductor packages provide much more sophisticated string handling utilities for sequence analysis (Lawrence et al., 2013, Huber et al., 2015).

• Biostrings: general sequence analysis environment
• ShortRead: pipeline for short read data
• IRanges: low-level infrastructure for range data
• GenomicRanges: high-level infrastructure for range data
• GenomicFeatures: managing transcript centric annotations
• GenomicAlignments: handling short genomic alignments
• Rsamtools: interface to samtools, bcftools and tabix
• BSgenome: genome annotation data
• biomaRt: interface to BioMart annotations
• rtracklayer: Annotation imports, interface to online genome browsers