Package: RWireX
Title: Co-accessibility analysis of scATAC-seq data to infer chromatin co-accessibility
Version: 1.1.06
Authors@R: 
    c(person(given = "Isabelle",
           family = "Seufert",
           role = c("aut", "cre"),
           email = "i.seufert@dkfz-heidelberg.de",
           comment = c(ORCID = "0000-0001-9811-3836")),
    person(given = "Anastasiya",
           family = "Vladimirova"))
Maintainer: Isabelle Seufert <i.seufert@dkfz-heidelberg.de>
Description: RWireX performs co-accessibility analysis of scATAC-seq data acquired by droplet-based single cell sequencing. It is based on our previously developed RWire package and implemented as an extension to the ArchR software package. RWireX employs a local background model, computes single-cell link activity scores, and provides co-accessibility maps of large genomic regions to identify domains of enriched co-accessibility. 
Depends:
    R (>= 4.1),
    ArchR (>= 1.0.1)
Imports:
    parallel,
    ggExtra,
    plotgardener,
    plyranges,
    SpectralTAD
License: `use_mit_license()`, `use_gpl3_license()` or friends to
    pick a license
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Collate: 
    'zzz.R'
    'coAccessibilityHelper.R'
    'getCoAccessibility.R'
    'getCoAccessibilityOnCustomMatrix.R'
    'getLinkActivityMatrix.R'
    'getBackgroundCoAccessibility.R'
    'getCoAccessibilityChromosomeWise.R'
    'getCoAccessibleDomains.R'
    'filterCoAccessibility.R'
    'plotBrowserTrack.R'
    'plotCoAccessibilityMap.R'
    'plotFeatureViolin.R'
    'downloadVignetteData.R'
