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Bioconductor - enhancerHomologSearch (development version)

enhancerHomologSearch

This is the development version of enhancerHomologSearch; for the stable release version, see enhancerHomologSearch.

Identification of putative mammalian orthologs to given enhancer

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-8652-2488 , Valentina Cigliola [dtc], Kenneth Poss [fnd]

Maintainer: Jianhong Ou <jou at morgridge.org>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("enhancerHomologSearch")

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("enhancerHomologSearch")
Details biocViews Alignment, GeneRegulation, Sequencing, Software Version 1.15.1 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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 System Requirements URL https://jianhong.github.io/enhancerHomologSearch Bug Reports https://github.com/jianhong/enhancerHomologSearch/issues See More 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 Linking To Rcpp 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.

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