spatzie

DOI: 10.18129/B9.bioc.spatzie    

Identification of enriched motif pairs from chromatin interaction data

Bioconductor version: Release (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>

Installation

To install this package, start R (version "4.2") 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")

 

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	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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_1.2.0.tar.gz
Windows Binary	spatzie_1.2.0.zip
macOS Binary (x86_64)	spatzie_1.2.0.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