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Analyze and interpret RNA-Seq results

Bioconductor version: Release (3.19)

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.

Author: Travis Blimkie [cre] , Andy An [aut]

Maintainer: Travis Blimkie <travis.m.blimkie at>

Citation (from within R, enter citation("pathlinkR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analyze and visualize RNA-Seq data with pathlinkR HTML R Script
Reference Manual PDF


biocViews GeneSetEnrichment, Network, NetworkEnrichment, Pathways, RNASeq, Reactome, Software
Version 1.0.1
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3 + file LICENSE
Depends R (>= 4.3.0)
Imports circlize, clusterProfiler, ComplexHeatmap, dplyr, ggforce, ggplot2, ggpubr, ggraph, ggrepel, grid, igraph, purrr, sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork
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Suggests AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr,, rmarkdown, scales, testthat (>= 3.0.0), vdiffr
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Follow Installation instructions to use this package in your R session.

Source Package pathlinkR_1.0.1.tar.gz
Windows Binary
macOS Binary (x86_64) pathlinkR_1.0.1.tgz
macOS Binary (arm64) pathlinkR_1.0.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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