spatzie

Identification of enriched motif pairs from chromatin interaction data

Bioconductor version: Release (3.17)

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	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 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
Linking To
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
System Requirements
Enhances
URL	https://spatzie.mit.edu

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Package Archives

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

Source Package	spatzie_1.6.0.tar.gz
Windows Binary	spatzie_1.6.0.zip
macOS Binary (x86_64)	spatzie_1.6.0.tgz
macOS Binary (arm64)	spatzie_1.6.0.tgz
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/
Package Downloads Report	Download Stats