Package: HiCExperiment
Title: Bioconductor class for interacting with Hi-C files in R
Version: 1.7.1
Date: 2022-11-10
Authors@R:
    c(person(given = "Jacques",
           family = "Serizay",
           role = c("aut", "cre"),
           email = "jacquesserizay@gmail.com",
           comment = c(ORCID = "0000-0002-4295-0624")))
Description: R generic interface to Hi-C contact matrices in `.(m)cool`, 
    `.hic` or HiC-Pro derived formats, as well as other Hi-C processed 
    file formats. Contact matrices can be partially parsed using a random access 
    method, allowing a memory-efficient representation of Hi-C data 
    in R. The `HiCExperiment` class stores the Hi-C contacts parsed from 
    local contact matrix files. `HiCExperiment` instances can be further 
    investigated in R using the `HiContacts` analysis package.
License: MIT + file LICENSE
URL: https://github.com/js2264/HiCExperiment
BugReports: https://github.com/js2264/HiCExperiment/issues
Depends:
    R (>= 4.2)
Imports:
    InteractionSet,
    strawr, 
    GenomeInfoDb,
    GenomicRanges,
    IRanges,
    S4Vectors,
    BiocGenerics,
    BiocIO,
    BiocParallel, 
    methods,
    rhdf5,
    Matrix,
    vroom,
    dplyr,
    stats
Suggests:
    HiContacts, 
    HiContactsData,
    BiocFileCache, 
    rtracklayer, 
    testthat (>= 3.0.0),
    BiocStyle,
    knitr,
    rmarkdown
biocViews:
    HiC,
    DNA3DStructure, 
    DataImport
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Collate: 
    'HiCExperiment-class.R'
    'AggrHiCExperiment-class.R'
    'AllGenerics.R'
    'HiCExperiment-methods.R'
    'AggrHiCExperiment-methods.R'
    'PairsFile-class.R'
    'ContactsFile-class.R'
    'ContactsFile-methods.R'
    'CoolFile-class.R'
    'CoolFile-methods.R'
    'HicFile-class.R'
    'HicFile-methods.R'
    'HicproFile-class.R'
    'HicproFile-methods.R'
    'PairsFile-methods.R'
    'import-methods.R'
    'available.R'
    'bin.R'
    'checks.R'
    'coerce.R'
    'data.R'
    'export-methods.R'
    'globals.R'
    'parse-cool.R'
    'parse-hic.R'
    'parse-hicpro.R'
    'parse-pairs.R'
    'parse-slices.R'
    'reexports.R'
    'utils.R'
    'zzz.R'