pathlinkR
Analyze and interpret RNA-Seq results
Bioconductor version: 3.23 · Package version: 1.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pathlinkR")Details
| Maintainer | Travis Blimkie <travis.m.blimkie@gmail.com> |
| Author | Travis Blimkie [cre] (ORCID: <https://orcid.org/0000-0001-8778-8627>), Andy An [aut] |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/hancockinformatics/pathlinkR |
| Bug Reports | https://github.com/hancockinformatics/pathlinkR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneSetEnrichment, Network, NetworkEnrichment, Pathways, RNASeq, Reactome, Software |
| Package Short Url | https://bioconductor.org/packages/pathlinkR/ |
Citation
From within R, enter citation("pathlinkR"):
Andy An. pathlinkR: Analyze and interpret RNA-Seq results. doi:10.18129/B9.bioc.pathlinkR, R package version 1.8.0, https://bioconductor.org/packages/pathlinkR.
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 | pathlinkR_1.8.0.tar.gz |
| Windows binary (x86_64) | pathlinkR_1.8.0.zip |
| macOS binary (arm64) | pathlinkR_1.8.0.tgz |
| macOS binary (x86_64) | pathlinkR_1.8.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: circlize, clusterProfiler, ComplexHeatmap, dplyr, fgsea, ggplot2, ggraph, ggrepel, grid, igraph, patchwork, purrr, sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork
Suggests: AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0)