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 (3.21)
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:
Maintainer: Jianhong Ou <jianhong.ou at duke.edu>
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")| enhancerHomologSearch Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, GeneRegulation, Sequencing, Software |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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.
| Source Package | enhancerHomologSearch_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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/ |
| Package Downloads Report | Download Stats |