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spatzie

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("spatzie")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("spatzie")
YY1 ChIA-PET motif analysis (single call) HTML
YY1 ChIA-PET motif analysis (step-by-step) HTML
Reference Manual PDF
NEWS Text

Details

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
System Requirements
URL https://spatzie.mit.edu
See More
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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Package Archives

Follow Installation instructions to use this package in your R session.

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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