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 (3.20)
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("spatzie")
):
Installation
To install this package, start R (version "4.4") 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.
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 | |
NEWS | Text |
Details
biocViews | Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software, Transcription |
Version | 1.11.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
License | GPL-3 |
Depends | R (>= 4.3) |
Imports | BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils |
System Requirements | |
URL | https://spatzie.mit.edu |
See More
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 | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | spatzie_1.11.0.tar.gz |
Windows Binary | spatzie_1.11.0.zip |
macOS Binary (x86_64) | spatzie_1.11.0.tgz |
macOS Binary (arm64) | |
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 |