Type: Package
Package: spatzie
Title: Identification of enriched motif pairs from chromatin
        interaction data
Version: 1.15.1
Authors@R: 
    c(person(given = "Jennifer",
             family = "Hammelman",
             role = c("aut", "cre", "cph"),
             email = "jhammelm@mit.edu",
             comment = c(ORCID = "0000-0002-1008-2666")),
      person(given = "Konstantin",
             family = "Krismer",
             role = "aut",
             email = "krismer@mit.edu",
             comment = c(ORCID = "0000-0001-8994-3416")),
      person(given = "David",
             family = "Gifford",
             role = c("ths", "cph"),
             email = "gifford@mit.edu",
             comment = c(ORCID = "0000-0003-1709-4034")))
Description: Identifies motifs that are significantly co-enriched from
    enhancer-promoter interaction data. While enhancer-promoter annotation
    is commonly used to define groups of interaction anchors, spatzie also
    supports co-enrichment analysis between preprocessed interaction
    anchors.  Supports BEDPE interaction data derived from genome-wide
    assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for
    differentially enriched motif pairs between two interaction
    experiments.
License: GPL-3
URL: https://spatzie.mit.edu
Depends: R (>= 4.3)
Imports: BiocGenerics, BSgenome, Seqinfo, GenomicFeatures,
        GenomicInteractions, GenomicRanges, ggplot2, IRanges,
        MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats,
        SummarizedExperiment, TFBSTools, utils
Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown,
        testthat, TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene,
        TxDb.Mmusculus.UCSC.mm9.knownGene
VignetteBuilder: knitr
biocViews: DNA3DStructure, GeneRegulation, PeakDetection, Epigenetics,
        FunctionalGenomics, Classification, HiC, Transcription
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
git_url: https://git.bioconductor.org/packages/spatzie
git_branch: devel
git_last_commit: 319405d
git_last_commit_date: 2025-07-23
Repository: Bioconductor 3.22
Date/Publication: 2025-07-24
NeedsCompilation: no
Packaged: 2025-07-25 02:33:21 UTC; biocbuild
Author: Jennifer Hammelman [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-1008-2666>),
  Konstantin Krismer [aut] (ORCID:
    <https://orcid.org/0000-0001-8994-3416>),
  David Gifford [ths, cph] (ORCID:
    <https://orcid.org/0000-0003-1709-4034>)
Maintainer: Jennifer Hammelman <jhammelm@mit.edu>
Built: R 4.5.1; ; 2025-07-25 14:23:32 UTC; windows
