DESCRIPTION

Package: CNEr 
Version: 1.33.1
Date: 2022-10-23
Title: CNE Detection and Visualization
Description: Large-scale identification and advanced visualization 
             of sets of conserved noncoding elements.
Author: Ge Tan <ge_tan@live.com>
Maintainer: Ge Tan <ge_tan@live.com>
Imports: Biostrings (>= 2.33.4),
         DBI (>= 0.7),
         RSQLite (>= 0.11.4),
         GenomeInfoDb (>= 1.1.3),
         GenomicRanges (>= 1.23.16),
         rtracklayer (>= 1.25.5),
         XVector (>= 0.5.4),
         GenomicAlignments (>= 1.1.9),
         methods,
         S4Vectors (>= 0.13.13),
         IRanges (>= 2.5.27),
         readr (>= 0.2.2),
         BiocGenerics,
         tools,
         parallel,
         reshape2 (>= 1.4.1),
         ggplot2 (>= 2.1.0),
         poweRlaw (>= 0.60.3),
         annotate (>= 1.50.0),
         GO.db (>= 3.3.0),
         R.utils (>= 2.3.0),
         KEGGREST (>= 1.14.0)
Depends: R (>= 3.4)
Suggests: Gviz (>= 1.7.4),
          BiocStyle,
          knitr,
          rmarkdown,
          testthat,
          BSgenome.Drerio.UCSC.danRer10,
          BSgenome.Hsapiens.UCSC.hg38,
          TxDb.Drerio.UCSC.danRer10.refGene,
          BSgenome.Hsapiens.UCSC.hg19,
          BSgenome.Ggallus.UCSC.galGal3
LinkingTo: S4Vectors, IRanges, XVector
VignetteBuilder: knitr
License: GPL-2 | file LICENSE
License_restricts_use: yes
URL: https://github.com/ge11232002/CNEr
BugReports: https://github.com/ge11232002/CNEr/issues
Type: Package
biocViews: GeneRegulation, Visualization, DataImport
NeedsCompilation: yes
LazyData: no
Collate: 
        GRangePairs-class.R
        GRangePairs-methods.R
        Axt-class.R
        CNE-class.R
        utils.R
        ceScan.R
        plot.R 
        makeGeneDbFromUCSC.R
        IO-methods.R
        scoringMatrix.R
        subAxt-methods.R
        Axt-methods.R
        DB.R
        AssemblyStats.R
        GRB.R
        WholeGenomeAlignment.R
        Ancora.R
        CNE-methods.R
        GO.R
        KEGG.R