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DESCRIPTION
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Package: gGnome
Title: gGnome: reference based assembly graph for analyzing rearranged genomes
Version: 0.1
Authors@R:
c(person("Xiaotong", "Yao", email = "[email protected]", role = c("aut", "cre")),
person("Marcin", "Imielinski", email = "[email protected]", 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.
Remotes:
github::mskilab/gUtils,
github::mskilab/gTrack,
github::mskilab/fishHook,
github::mskilab/bamUtils,
github::mskilab/gChain,
bioc::3.10/S4Vectors,
bioc::3.10/GenomicRanges,
bioc::3.10/rtracklayer,
bioc::3.10/VariantAnnotation,
bioc::3.10/Biostrings,
bioc::3.10/GenomeInfoDb
Depends:
R (>= 3.5.0),
data.table (>= 1.11),
igraph,
Matrix,
gTrack,
gUtils,
reshape2,
GenomicRanges,
Imports:
methods,
R6,
VariantAnnotation,
rtracklayer,
RCurl,
jsonlite,
stringr,
gChain,
fishHook
Suggests:
testthat (>= 2.0),
circlize,
covr,
reshape,
Biostrings,
ape,
bamUtils,
arrow
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2