spatzie

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see spatzie.

Identification of enriched motif pairs from chromatin interaction data

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software, Transcription

Version 1.0.1

In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)

License GPL-3

Depends R (>= 4.1)

Imports BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils

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

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Build Report Build Report

Package Archives

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

Source Package spatzie_1.0.1.tar.gz

Windows Binary spatzie_1.0.1.zip

macOS 10.13 (High Sierra) spatzie_1.0.1.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

Old Source Packages for BioC 3.14 Source Archive