Package: enhancerHomologSearch
Type: Package
Title: Identification of putative mammalian orthologs to given enhancer
Version: 1.3.4
Authors@R: c(person(given="Jianhong", family="Ou", email="jianhong.ou@duke.edu", 
                 role=c("aut", "cre"), comment=c(ORCID="0000-0002-8652-2488")),
            person(given="Valentina", family="Cigliola", role=c("dtc")),
            person(given="Kenneth", family="Poss", role=c("fnd")))
Description: Get ENCODE data of enhancer region via H3K4me1 peaks and
             search homolog regions for given sequences. The candidates
             of enhancer homolog regions can be filtered by distance to
             target TSS. The top candidates from human and mouse will be
             aligned to each other and then exported as multiple alignments
             with given enhancer.
BugReports: https://github.com/jianhong/enhancerHomologSearch/issues
URL: https://jianhong.github.io/enhancerHomologSearch
Depends: R (>= 4.1.0), methods
Imports: BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache,
         GenomeInfoDb, GenomicRanges,
         httr,
         IRanges,
         jsonlite,
         motifmatchr,
         Matrix,
         rtracklayer, Rcpp,
         S4Vectors, stats,
         utils
Suggests: knitr, rmarkdown,
  BSgenome.Drerio.UCSC.danRer10,
  BSgenome.Hsapiens.UCSC.hg38,
  BSgenome.Mmusculus.UCSC.mm10,
  TxDb.Hsapiens.UCSC.hg38.knownGene,
  org.Hs.eg.db,
  TxDb.Mmusculus.UCSC.mm10.knownGene,
  org.Mm.eg.db,
  MotifDb,
  testthat,
  TFBSTools
biocViews: Sequencing, GeneRegulation, Alignment
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.2.0
LinkingTo: Rcpp