linkSet: Base Classes for Storing Genomic Link Data

The linkSet package provides tools for working with genomic link sets, which represent connections between different genomic regions. This package is designed for bioinformatics and genomic data analysis, offering various methods to manipulate and analyze linkSet objects.

Details

The main class provided by this package is the linkSet class, which is designed to represent and analyze genomic interactions, particularly focusing on gene-enhancer relationships. Key features include:

• Representation of genomic interactions with two types of anchors: "bait" (typically genes) and "other end" (typically enhancers or other regulatory elements).

• Flexible input methods, supporting construction from various data types.

• Metadata storage for additional information about interactions.

• Integration with Bioconductor classes and tools.

• Methods for annotating promoters and distinguishing between inter- and intra-chromosomal interactions.

References

Add any relevant references here.

See also

Useful links:

• https://github.com/GilbertHan1011/linkSet

• Report bugs at https://github.com/GilbertHan1011/linkSet/issues/new

Examples

# Basic usage example
library(linkSet)
# Add a simple example here