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pathlinkR

This is the development version of pathlinkR; to use it, please install the devel version of Bioconductor.

Analyze and interpret RNA-Seq results


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("pathlinkR")

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("pathlinkR")
Analyze and visualize RNA-Seq data with pathlinkR HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneSetEnrichment, Network, NetworkEnrichment, Pathways, RNASeq, Reactome, Software
Version 0.99.382
In Bioconductor since BioC 3.19 (R-4.4)
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
System Requirements
URL https://github.com/hancockinformatics/pathlinkR
Bug Reports https://github.com/hancockinformatics/pathlinkR/issues
See More
Suggests AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0), vdiffr
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pathlinkR_0.99.382.tar.gz
Windows Binary pathlinkR_0.99.382.zip
macOS Binary (x86_64) pathlinkR_0.99.382.tgz
macOS Binary (arm64) pathlinkR_0.99.381.tgz
Source Repository git clone https://git.bioconductor.org/packages/pathlinkR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pathlinkR
Bioc Package Browser https://code.bioconductor.org/browse/pathlinkR/
Package Short Url https://bioconductor.org/packages/pathlinkR/
Package Downloads Report Download Stats