bedtoolsr

bedtoolsr provides a direct R interface to the bedtools suite to manipulate and analyze genomic interval and DNA sequencing–derived datasets.

Key Features:

• Direct bedtools interface: Uses the version of bedtools installed on the host system to expose bedtools functionality to R.
• Input/output flexibility: Supports both file paths and R objects as inputs and outputs.
• Automatic format detection: Detects input and output formats automatically.
• Compatibility: Targets compatibility with past and future versions of bedtools.
• Unit tests: Includes unit tests to support stability and reliability.

Scientific Applications:

• Genomic interval manipulation: Performs complex set operations on genomic intervals.
• Identification of regions of interest: Identifies genomic regions of interest from genomic datasets.
• Sequence alignment analysis: Analyzes sequence alignments derived from DNA sequencing.
• Large-scale genomic data handling: Manipulates and processes large-scale genomic datasets generated by DNA sequencing technologies.

Methodology:

Invokes the system-installed bedtools executables from R, accepts file paths or R objects as inputs and outputs, automatically detects input/output formats, includes unit tests, and targets compatibility across bedtools versions.