valr

valr provides functions for manipulation and analysis of genomic intervals and associated signals within the R environment for reproducible exploratory analysis of large genomic datasets.

Key Features:

• Integration with tidyverse: Built upon the tidyverse collection of R packages and specifically leverages dplyr for data manipulation of interval data.
• Performance: Benchmarks report performance comparable to BEDtools for handling large-scale genomic intervals.
• Interactive analysis: Supports interactive workflows that enable dynamic exploration and visualization of genome-scale data within R.
• Pipeline integration: Designed to be incorporated into genomic analysis pipelines and to interoperate with other bioinformatics tools.

Scientific Applications:

• Genomic interval operations: Perform interval operations such as merging, intersecting, and subtracting genomic intervals.
• Signal processing: Analyze signals associated with genomic regions to investigate regulatory elements and other functional genomics features.
• Data visualization: Generate plots and graphics using R visualization capabilities to aid interpretation of genomic data.

Methodology:

Implements interval-based operations using tidyverse data manipulation tools, particularly dplyr, to support reproducible and efficient analyses.