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Identification of putative mammalian orthologs to given enhancer

Bioconductor version: Release (3.19)

Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.

Author: Jianhong Ou [aut, cre] , Valentina Cigliola [dtc], Kenneth Poss [fnd]

Maintainer: Jianhong Ou <jianhong.ou at>

Citation (from within R, enter citation("enhancerHomologSearch")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

enhancerHomologSearch Vignette HTML R Script
Reference Manual PDF


biocViews Alignment, GeneRegulation, Sequencing, Software
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL (>= 2)
Depends R (>= 4.1.0), methods
Imports BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, pwalign, rtracklayer, Rcpp, S4Vectors, stats, utils
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Suggests knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene,, TxDb.Mmusculus.UCSC.mm10.knownGene,, MotifDb, testthat, TFBSTools
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Source Package enhancerHomologSearch_1.10.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) enhancerHomologSearch_1.10.0.tgz
macOS Binary (arm64)
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Source Repository (Developer Access) git clone
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