Package: generegulation
Title: Finding Candidate Binding Sites for Known Transcription Factors
        via Sequence Matching
Version: 1.36.0
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/
git_url: https://git.bioconductor.org/packages/generegulation
git_branch: RELEASE_3_23
git_last_commit: bccda2d
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-06-02
Packaged: 2026-06-02 17:06:06 UTC; biocbuild
Author: Bioconductor Package Maintainer [aut, cre]
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
