spatzie

DOI: 10.18129/B9.bioc.spatzie    

This is the development version of spatzie; for the stable release version, see spatzie.

Identification of enriched motif pairs from chromatin interaction data

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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

Details

biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software, Transcription
Version 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 4.1)
Imports BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils
LinkingTo
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
SystemRequirements
Enhances
URL https://spatzie.mit.edu
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package spatzie_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) spatzie_1.1.0.tgz
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: