Given a database of DNA sequence motifs representing transcription factors and enhancer promoter interaction data, spatzie performs statistical analysis to identify co-enriched transcription factors.
The spatzie package is part of Bioconductor since release 3.14. To install it on your system, enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("spatzie")
Alternatively, the latest version can be installed directly from this repository:
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github("jhammelman/spatzie", build_vignettes = TRUE)
Note: For most use cases it is not necessary to install the spatzie package locally, as a substantial part of its functionality is offered as an online service at https://spatzie.mit.edu.
For interaction data aligned to the most recent human or mouse genome assemblies (hg38, hg19, mm10, or mm9), the most common spatzie use cases are covered by the function find_ep_coenrichment, which is prominently featured in one of the vignettes:
vignette("single-call", package = "spatzie")
The functionality displayed in the vignette above is also available online at spatzie.mit.edu.
If more flexibility is required, e.g., different genome assemblies, locally cached promoter annotations, non-standard ways to filter interactions, this vignette is a good starting point:
vignette("individual-steps", package = "spatzie")
| Platform | Status |
|---|---|
| Travis CI |  |
| Bioconductor 3.18 (release) |  |
| Bioconductor 3.19 (devel) |  |
If you use spatzie in your research, please cite:
spatzie: An R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions
Jennifer Hammelman, Konstantin Krismer, and David K. Gifford
Nucleic Acids Research, Volume 50, Issue 9, 20 May 2022, Page e52; DOI: https://doi.org/10.1093/nar/gkac036
The development of this method was supported by National Institutes of Health (NIH) grants 1R01HG008754 and 1R01NS109217, and a National Science Foundation Graduate Research Fellowship (1122374).