The GxG package provides a flexible, queriable R interface to genome matrices (i.e. matrices of genomic ranges), such as those used to represent maps of 3D chromatin contacts or linked-read barcode sharing. 

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

Glocal streaming assembly for somatic and germline structural variant detection.

R package for applying Gamma-Poisson regression to identify statistical enrichment of somatic mutations in regions after correcting for genomic covariates.

R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

R API for building, manipulating, querying, and mining reference-aligned genome graphs within GenomicRanges framework.

D3.js-based dynamic visualization framework of reference-aligned genome graphs and assemblies

Syntactic sugar for GenomicRanges ninjas.

Lightweight R-based genomics workflow management for SGE, UGER, and LSF

GenomicRanges based R class for fast, out-of-core memory access and storage of numeric and character data that is a function of genomic position.