enhancerHomologSearch

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see enhancerHomologSearch.

Identification of putative mammalian orthologs to given enhancer

DOI: 10.18129/B9.bioc.enhancerHomologSearch

Bioconductor version: 3.21

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 iD 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")
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")

enhancerHomologSearch Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, GeneRegulation, Sequencing, Software

Version 1.14.0

In Bioconductor since BioC 3.14 (R-4.1) (4 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

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

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package enhancerHomologSearch_1.14.0.tar.gz

Windows Binary (x86_64) enhancerHomologSearch_1.14.0.zip

macOS Binary (x86_64) enhancerHomologSearch_1.14.0.tgz

macOS Binary (arm64) enhancerHomologSearch_1.14.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/enhancerHomologSearch

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/enhancerHomologSearch

Bioc Package Browser https://code.bioconductor.org/browse/enhancerHomologSearch/

Package Short Url https://bioconductor.org/packages/enhancerHomologSearch/

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