pathlinkR
This is the development version of pathlinkR; for the stable release version, see pathlinkR.
Analyze and interpret RNA-Seq results
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Travis Blimkie <travis.m.blimkie at gmail.com>
citation("pathlinkR")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneSetEnrichment, Network, NetworkEnrichment, Pathways, RNASeq, Reactome, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | circlize, clusterProfiler, ComplexHeatmap, dplyr, fgsea, 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 | |
| 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 | pathlinkR_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |