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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/annoLinker/ |
| Package Short Url | https://bioconductor.org/packages/annoLinker/ |
| Package Downloads Report | Download Stats |