R Observatory: Metrics for spatzie version 1.18.0

Balamuta, James Joseph

spatzie

Bioc current

Identification of enriched motif pairs from chromatin interaction data

v1.18.0 · software · GPL-3

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Release Lineage

Entered 3.14 · Oct 27, 2021

Current · Requires R 4.6

1.0 In 10 of 49 releases 3.23

Description

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.

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Topics

Software › BiologicalQuestion › DNA3DStructure

Software › BiologicalQuestion › GeneRegulation

Software › BiologicalQuestion › PeakDetection

Software › ResearchField › Epigenetics

Software › ResearchField › FunctionalGenomics

Software › StatisticalMethod › Classification

Software › Technology › Sequencing › HiC

Software › AssayDomain › Transcription

People

Jennifer Hammelman author maintainer cph
David Gifford ths cph
Konstantin Krismer author

Cite

Cite this package

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citation("spatzie")

Bioconductor packages have no CRAN DOI. The package landing page is https://bioconductor.org/packages/spatzie.

BibTeX, derived from DESCRIPTION

@Manual{spatzie,
  title  = {spatzie: Identification of enriched motif pairs from chromatin
interaction data},
  author = {Hammelman, Jennifer and Gifford, David and Krismer, Konstantin},
  year   = {2026},
  note   = {R package version 1.18.0},
  url    = {https://bioconductor.org/packages/spatzie}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

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BibTeX

@misc{robservatoryspatzie,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {spatzie} version 1.18.0},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/bioc/spatzie},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for spatzie version 1.18.0 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/bioc/spatzie

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for spatzie version 1.18.0
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/bioc/spatzie
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/bioc/spatzie.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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