DOI: 10.18129/B9.bioc.spatzie  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see spatzie.

Identification of enriched motif pairs from chromatin interaction data

Bioconductor version: 3.16

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.

Author: Jennifer Hammelman [aut, cre, cph] , Konstantin Krismer [aut] , David Gifford [ths, cph]

Maintainer: Jennifer Hammelman <jhammelm at>

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HTML YY1 ChIA-PET motif analysis (single call)
HTML YY1 ChIA-PET motif analysis (step-by-step)
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biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software, Transcription
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL-3
Depends R (>= 4.1)
Imports BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils
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