DESCRIPTION

Package: gGnome
Title: gGnome: reference based assembly graph for analyzing rearranged genomes
Version: 0.1
Authors@R:
	c(person("Xiaotong", "Yao", email = "xiaotong.yao23@gmail.com", role = c("aut", "cre")),
	person("Marcin", "Imielinski", email = "mai9037@med.cornell.edu", role = c("aut"),
  ))
Description: The gGnome package provides a flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in the R6 object oriented standard and built around a powerful GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges.
NeedsCompilation: yes
Remotes: 
  github::mskilab-org/gUtils,
  github::mskilab-org/gTrack,
  github::mskilab-org/fishHook,
  github::mskilab-org/bamUtils,
  github::mskilab-org/gChain,
  github::Bioconductor/VariantAnnotation
Depends:
    R (>= 4.0.0),
    data.table (>= 1.14),
    igraph,
    Matrix,
    gTrack,
    gUtils,     
    reshape2,
    GenomicRanges
Imports:
    methods,
    R6,
    VariantAnnotation,
    rtracklayer,
    RCurl,
    jsonlite,
    stringr,
    gChain,
    fishHook,
    forcats,
    IRanges,
    GenomeInfoDb,
    BiocGenerics,
    S4Vectors
Suggests: 
  testthat (>= 2.0),
  circlize,
  covr,
  reshape,
  Biostrings,
  ape,
  bamUtils,
  arrow
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3