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Identification of enriched motif pairs from chromatin interaction data

Bioconductor version: Release (3.18)

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 mit.edu>

Citation (from within R, enter citation("spatzie")):


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if (!require("BiocManager", quietly = TRUE))


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YY1 ChIA-PET motif analysis (single call) HTML
YY1 ChIA-PET motif analysis (step-by-step) HTML
Reference Manual PDF


biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software, Transcription
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.3)
Imports BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils
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URL https://spatzie.mit.edu
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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
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Source Package spatzie_1.8.0.tar.gz
Windows Binary spatzie_1.8.0.zip
macOS Binary (x86_64) spatzie_1.8.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/spatzie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spatzie
Bioc Package Browser https://code.bioconductor.org/browse/spatzie/
Package Short Url https://bioconductor.org/packages/spatzie/
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