rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq...

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• The R environment is a leading platform for statistical analysis of biological data.
• Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) formats are standard for storing sequence alignment data.
• R users require efficient tools to interact with BAM files for biological data exploration.

Purpose of the Study:

• To introduce rbamtools, an R package providing full accessibility to BAM files.
• To enable seamless reading, writing, subsetting, and plotting of BAM data within R.
• To facilitate the tabulation of splicing events across multiple BAM files.

Main Methods:

• Development of an R package, rbamtools, with syntax mirroring the SAM/BAM format.
• Implementation of functions for direct manipulation of BAM file content.
• Integration of capabilities for accumulative tabulation of splicing events.

Main Results:

• rbamtools offers a comprehensive interface for BAM file access in R.
• The package supports essential operations like data reading, writing, subset extraction, and alignment depth plotting.
• Efficient tabulation of splicing events across numerous BAM files is achievable.

Conclusions:

• rbamtools significantly enhances the utility of R for analyzing sequence alignment data.
• The package provides R users with powerful and user-friendly tools for BAM file manipulation.
• Facilitates advanced analyses such as splicing event quantification in large-scale genomic studies.