Package: enhancerHomologSearch
Type: Package
Title: Identification of putative mammalian orthologs to given enhancer
Version: 1.17.0
Authors@R: c(person(given="Jianhong", family="Ou", email="jou@morgridge.org", 
                 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, Seqinfo, GenomicRanges, httr, IRanges, jsonlite,
        motifmatchr, Matrix, pwalign, rtracklayer, Rcpp, S4Vectors,
        stats, utils
Suggests: GenomeInfoDb, 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: 7.3.2
LinkingTo: Rcpp
Config/pak/sysreqs: make libgsl0-dev libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:11:19 UTC
RemoteUrl: https://github.com/bioc/enhancerHomologSearch
RemoteRef: HEAD
RemoteSha: aec981004b80c9f126981dff80e92d8e14b0f648
NeedsCompilation: yes
Packaged: 2025-11-13 21:01:17 UTC; root
Author: Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>),
  Valentina Cigliola [dtc],
  Kenneth Poss [fnd]
Maintainer: Jianhong Ou <jou@morgridge.org>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-11-13 21:11:20 UTC; windows
Archs: x64
