DESCRIPTION

Package: TFregulomeR
Type: Package
Title: TFregulomeR reveals transcription factors’ context-specific features and functions
Version: 2.0.0
Description: An R-package linked to a large timely-updated compendium of cistrome and methylome datasets, implemented with functionalities that facilitate the manipulation and analysis of TFBS and methylome meta-data. In particular, TFregulomeR permits the characterisation of TF binding partners and cell-specific TFBSs, along with the study of TF’s functions in the context of different partners’ combinations and DNA methylation levels.
Authors@R: c(person("Quy Xiao Xuan", "Lin", email = "linquyzju@gmail.com", role = c("aut", "cre")), 
             person("Denis", "Thieffry", email = "denis.thieffry@ens.fr", role = "ctb"),
             person("Sudhakar", "Jha", email = "csisjha@nus.edu.sg", role = "ctb"),
              person("Touati", "Benoukraf", email = "tbenoukraf@mun.ca", role = "aut"))
Depends: R (>= 3.6.0), methods
Imports: graphics,
         grDevices,
         utils,
         jsonlite (>= 1.5), 
         ggplot2 (>= 3.0.0), 
         ggseqlogo (>= 0.1), 
         gridExtra (>= 2.3), 
         grid (>= 3.6.0),
         IRanges (>= 2.14.12), 
         S4Vectors (>= 0.18.3), 
         GenomicRanges (>= 1.32.7),
         curl (>= 3.2),
         gplots (>= 3.0.1.1)
License: GPL-3.0
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: 
    knitr,
    rmarkdown,
    rGREAT (>= 1.16.1),
    rtracklayer (>= 1.42.1),
    rbokeh (>= 0.5.0),
    TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.0),
    TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2),
    TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.4),
    TxDb.Mmusculus.UCSC.mm9.knownGene (>= 3.2.2),
    TFBSTools (>= 1.20.0),
    GenomeInfoDb (>= 1.18.1),
    BiocGenerics (>= 0.28.0),
    RUnit,
    GenomicFeatures (>= 1.34.2)
biocViews: MotifAnnotation, Epigenetics, ChIPSeq, MethylSeq, Transcription, DNAMethylation
VignetteBuilder: knitr
BugReports: https://github.com/benoukraflab/TFregulomeR/issues