annoLinker
This is the released version of annoLinker; for the devel version, see annoLinker.
Annotating genomic regions through chromatin interaction links
Bioconductor version: Release (3.23)
Fast annotation of genomic peaks using DNA interaction data by constructing interaction networks with igraph, where peaks overlapping any node in a connected subgraph are annotated with all genes in that subgraph. The annotation evidence could be visualized as either a network graph or a genomic track integrated with gene annotation information.
Author: Jianhong Ou [aut, cre] 
, Kenneth Poss [aut, fnd]
Maintainer: Jianhong Ou <jou at morgridge.org>
citation("annoLinker")):Jianhong Ou, Kenneth Poss. annoLinker: Annotating genomic regions through chromatin interaction links. doi:10.18129/B9.bioc.annoLinker, R package version 1.0.0, https://bioconductor.org/packages/annoLinker.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("annoLinker")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("annoLinker")| annoLinker Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Network, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | AnnotationDbi, BiocGenerics, future.apply, GenomicRanges, GenomeInfoDb, igraph, IRanges, InteractionSet, methods, progressr, S4Vectors, Seqinfo, trackViewer, visNetwork |
| System Requirements | |
| URL | https://github.com/jianhong/annoLinker |
| Bug Reports | https://github.com/jianhong/annoLinker/issues |
See More
| Suggests | BiocStyle, knitr, rtracklayer, rmarkdown, testthat, TxDb.Drerio.UCSC.danRer10.refGene, org.Dr.eg.db, future |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | annoLinker_1.0.0.tar.gz |
| Windows Binary (x86_64) | annoLinker_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | annoLinker_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | annoLinker_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/annoLinker |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/annoLinker |
| Package Short Url | https://bioconductor.org/packages/annoLinker/ |
| Package Downloads Report | Download Stats |