spatzie

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see spatzie.

All versions

3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

Identification of enriched motif pairs from chromatin interaction data

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-1008-2666 , Konstantin Krismer [aut] ORCID: 0000-0001-8994-3416 , David Gifford [ths, cph] ORCID: 0000-0003-1709-4034

Maintainer: Jennifer Hammelman <jhammelm at mit.edu>

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

Jennifer Hammelman, Konstantin Krismer. spatzie: Identification of enriched motif pairs from chromatin interaction data. doi:10.18129/B9.bioc.spatzie, R package version 1.18.0, https://bioconductor.org/packages/spatzie.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software, Transcription
Version	1.18.0
In Bioconductor since	BioC 3.14 (R-4.1) (5 years)
License	GPL-3
Depends	R (>= 4.3)
Imports	BiocGenerics, BSgenome, Seqinfo, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils
System Requirements
URL	https://spatzie.mit.edu

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
Linking To
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Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/spatzie
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/spatzie
Package Short Url	https://bioconductor.org/packages/spatzie/
Package Downloads Report	Download Stats