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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 |
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) | |
| 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 |