This is the development version of spatzie; for the stable release version, see spatzie.
Identification of enriched motif pairs from chromatin interaction dataBioconductor version: Development (3.22)
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, entercitation("spatzie")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("spatzie")Follow Installation instructions to use this package in your R session.
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