Package: GPlinksR 0.99.0

Xinran Wang

GPlinksR: Building Gene-Peak Network for ATAC-RNA Integration

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.

Authors:Xinran Wang [aut, cre], Kelly Street [ctb], Huaiyu Mi [ctb], Bryan Queme [ctb]

GPlinksR_0.99.0.tar.gz
GPlinksR_0.99.0.zip(r-4.7)GPlinksR_0.99.0.zip(r-4.6)GPlinksR_0.99.0.zip(r-4.5)
GPlinksR_0.99.0.tgz(r-4.6-any)GPlinksR_0.99.0.tgz(r-4.5-any)
GPlinksR_0.99.0.tar.gz(r-4.7-any)GPlinksR_0.99.0.tar.gz(r-4.6-any)
GPlinksR_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GPlinksR/json (API)
NEWS

# Install 'GPlinksR' in R:

install.packages('GPlinksR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/corawang123/gplinksr/issues

Datasets:

gp_example_inputs - Example Gene and Peak Inputs for GPlinksR
gp_example_links - Example Link Table for the Packaged GPlinksR Demo Subset

On CRAN:

geneexpression network sequencing transcriptomics

3.60 score 2 scripts 3 exports 98 dependencies

Last updated from:f87b135092. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	195
linux-devel-x86_64	OK	229
source / vignettes	OK	246
linux-release-x86_64	OK	210
macos-release-arm64	OK	108
macos-oldrel-arm64	OK	117
windows-devel	OK	167
windows-release	OK	164
windows-oldrel	OK	179
wasm-release	OK	205

Exports:build_gp_links build_gp_links_wrapper get_peregrine_file

Dependencies:abind AnnotationDbi AnnotationFilter askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr EnsDb.Hsapiens.v86 ensembldb fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment openssl pillar pkgconfig png prettyunits progress ProtGenerics purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XML xml2 XVector yaml

GPlinksR: Building Gene-Peak Links from Simulated Single-Cell Inputs

Xinran Wang, Kelly Street, Huaiyu Mi, and Bryan Queme

Rendered fromGPlinksR.Rmdusingknitr::rmarkdownon Jun 23 2026.

Last update: 2026-03-28
Started: 2026-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build Gene-Peak Network (Enhancer, Promoter, Closest)	build_gp_links
Build Gene-Peak Links from MAE or SCE Input	build_gp_links_wrapper
Download Enhancer-Gene Link File from PANTHER Peregrine Database	get_peregrine_file
Example Gene and Peak Inputs for GPlinksR	gp_example_inputs
Example Link Table for the Packaged GPlinksR Demo Subset	gp_example_links