GPlinksR
This is the development version of GPlinksR; to use it, please install the devel version of Bioconductor.
Building Gene-Peak Network for ATAC-RNA Integration
Bioconductor version: Development (3.24)
GPlinksR constructs gene-peak regulatory networks for ATAC-RNA integration by combining enhancer-based, promoter-based, and proximity (closest-gene) mappings. The package accepts direct peak and gene vectors as well as container-based inputs through a wrapper for common Bioconductor object classes. Enhancer-gene links are obtained from the PEREGRINE enhancer-gene datasets provided by AnnoQ, while promoter and gene coordinates are retrieved from EnsDb.Hsapiens.v86.
Author: Xinran Wang [aut, cre]
, Kelly Street [ctb], Huaiyu Mi [ctb], Bryan Queme [ctb]
Maintainer: Xinran Wang <xwang210 at usc.edu>
citation("GPlinksR")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GPlinksR")
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("GPlinksR")| GPlinksR: Gene-Peak Links from Example Inputs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Network, Sequencing, Software, Transcriptomics |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | BiocFileCache, data.table, GenomicRanges, GenomeInfoDb, IRanges, methods, MultiAssayExperiment, S4Vectors, EnsDb.Hsapiens.v86, ensembldb, biomaRt, dplyr, SingleCellExperiment, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/Corawang123/GPlinksR |
| Bug Reports | https://github.com/Corawang123/GPlinksR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| 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 | GPlinksR_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | GPlinksR_0.99.2.tgz |
| macOS Binary (sonoma-arm64) | GPlinksR_0.99.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GPlinksR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GPlinksR |
| Bioc Package Browser | https://code.bioconductor.org/browse/GPlinksR/ |
| Package Short Url | https://bioconductor.org/packages/GPlinksR/ |
| Package Downloads Report | Download Stats |