Package: generegulation
Title: Finding Candidate Binding Sites for Known Transcription Factors
        via Sequence Matching
Version: 1.37.0
Date: 2017-09-05
Authors@R: c(person(role=c("aut", "cre"), "Bioconductor Package Maintainer", email = "maintainer@bioconductor.org"))
Description: The binding of transcription factor proteins (TFs) to DNA
        promoter regions upstream of gene transcription start sites
        (TSSs) is one of the most important mechanisms by which gene
        expression, and thus many cellular processes, are controlled.
        Though in recent years many new kinds of data have become
        available for identifying transcription factor binding sites
        (TFBSs) -- ChIP-seq and DNase I hypersensitivity regions among
        them -- sequence matching continues to play an important role.
        In this workflow we demonstrate Bioconductor techniques for
        finding candidate TF binding sites in DNA sequence using the
        model organism Saccharomyces cerevisiae.  The methods
        demonstrated here apply equally well to other organisms.
Depends: R (>= 3.3.0), BSgenome.Scerevisiae.UCSC.sacCer3, Biostrings,
        GenomicFeatures, MotifDb, S4Vectors,
        TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, motifStack,
        org.Sc.sgd.db, seqLogo
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: Workflow, EpigeneticsWorkflow
Suggests: knitr, rmarkdown, BiocStyle
NeedsCompilation: no
URL: https://www.bioconductor.org/help/workflows/generegulation/
Config/pak/sysreqs: cmake make libgsl0-dev libbz2-dev liblzma-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:40:31 UTC
RemoteUrl: https://github.com/bioc/generegulation
RemoteRef: HEAD
RemoteSha: b530c74deae42abd19ec3dc1e6887b8e1b1a01f5
Packaged: 2026-10-31 12:08:25 UTC; root
Author: Bioconductor Package Maintainer [aut, cre]
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>