The open source environment R isf the most widely used software to statistically explore biological data sets including sequence alignments. BAM is the de facto standard file format for sequence alignment. With rbamtools, we provide now a full spectrum of accessibility to BAM for R users such as reading, writing, extraction of subsets and plotting of alignment depth where the script syntax closely follows the SAM/BAM format. Additionally, rbamtools enables fast accumulative tabulation of splicing events over multiple BAM files.