DOI: 10.18129/B9.bioc.enhancerHomologSearch  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see enhancerHomologSearch.

Identification of putative mammalian orthologs to given enhancer

Bioconductor version: 3.16

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 duke.edu>

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


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biocViews Alignment, GeneRegulation, Sequencing, Software
Version 1.4.2
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL (>= 2)
Depends R (>= 4.1.0), methods
Imports BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, rtracklayer, Rcpp, S4Vectors, stats, utils
LinkingTo Rcpp
Suggests knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools
URL https://jianhong.github.io/enhancerHomologSearch
BugReports https://github.com/jianhong/enhancerHomologSearch/issues
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Source Package enhancerHomologSearch_1.4.2.tar.gz
Windows Binary enhancerHomologSearch_1.4.2.zip (64-bit only)
macOS Binary (x86_64) enhancerHomologSearch_1.4.2.tgz
macOS Binary (arm64) enhancerHomologSearch_1.4.2.tgz
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Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/enhancerHomologSearch
Bioc Package Browser https://code.bioconductor.org/browse/enhancerHomologSearch/
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