annoLinker
Annotating genomic regions through chromatin interaction links
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("annoLinker")Details
| Maintainer | Jianhong Ou <jou@morgridge.org> |
| Author | Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>), Kenneth Poss [aut, fnd] |
| License | GPL-3 |
| URL | https://github.com/jianhong/annoLinker |
| Bug Reports | https://github.com/jianhong/annoLinker/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Network, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/annoLinker/ |
Citation
From within R, enter 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.
Documentation
Download
Follow the 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 (arm64) | annoLinker_1.0.0.tgz |
| macOS binary (x86_64) | annoLinker_1.0.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: AnnotationDbi, BiocGenerics, future.apply, GenomicRanges, GenomeInfoDb, igraph, IRanges, InteractionSet, methods, progressr, S4Vectors, Seqinfo, trackViewer, visNetwork
Suggests: BiocStyle, knitr, rtracklayer, rmarkdown, testthat, TxDb.Drerio.UCSC.danRer10.refGene, org.Dr.eg.db, future