DESCRIPTION

Type: Package
Package: spatzie
Title: Identification of enriched motif pairs from chromatin interaction
    data
Version: 1.9.0
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,
    GenomeInfoDb,
    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