enhancerHomologSearch

DOI: 10.18129/B9.bioc.enhancerHomologSearch    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see enhancerHomologSearch.

Identification of putative mammalian orthologs to given enhancer

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	enhancerHomologSearch Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, GeneRegulation, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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
SystemRequirements
Enhances
URL	https://jianhong.github.io/enhancerHomologSearch
BugReports	https://github.com/jianhong/enhancerHomologSearch/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	enhancerHomologSearch_1.2.0.tar.gz
Windows Binary	enhancerHomologSearch_1.2.0.zip
macOS Binary (x86_64)	enhancerHomologSearch_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/enhancerHomologSearch
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/enhancerHomologSearch
Package Short Url	https://bioconductor.org/packages/enhancerHomologSearch/
Package Downloads Report	Download Stats