spatzie
Identification of enriched motif pairs from chromatin interaction data
Bioconductor version: Release (3.19)
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")
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 | 1.10.0 |
| 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_1.10.0.tar.gz |
| Windows Binary (x86_64) | spatzie_1.10.0.zip (64-bit only) |
| macOS Binary (x86_64) | spatzie_1.10.0.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 |
| Old Source Packages for BioC 3.19 | Source Archive |