Package: pathlinkR 1.9.5

Travis Blimkie

pathlinkR: Analyze and interpret RNA-Seq results

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.

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

pathlinkR_1.9.5.tar.gz
pathlinkR_1.9.5.zip(r-4.7)pathlinkR_1.9.5.zip(r-4.6)pathlinkR_1.9.5.zip(r-4.5)
pathlinkR_1.9.5.tgz(r-4.6-any)pathlinkR_1.9.5.tgz(r-4.5-any)
pathlinkR_1.9.5.tar.gz(r-4.7-any)pathlinkR_1.9.5.tar.gz(r-4.6-any)
pathlinkR_1.9.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pathlinkR/json (API)

# Install 'pathlinkR' in R:

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

Bug tracker:https://github.com/hancockinformatics/pathlinkr/issues

Datasets:

exampleDESeqResults - List of example results from DESeq2
groupedPathwayColours - Colour assignments for grouped pathways
hallmarkDatabase - Table of Hallmark gene sets and their genes
innateDbPPI - InnateDB PPI data
keggDatabase - Table of KEGG pathways and genes
mappingFile - Table of human gene ID mappings
pathwayCategories - Top-level pathway categories
reactomeDatabase - Table of all Reactome pathways and genes
sigoraDatabase - Table of all Sigora pathways and their constituent genes
sigoraExamples - Sigora enrichment example

On BioConductor:pathlinkR-1.9.0(bioc 3.24)pathlinkR-1.8.0(bioc 3.23)

genesetenrichment network pathways reactome rnaseq networkenrichment bioinformatics networks pathway-enrichment-analysis visualization

6.51 score 32 stars 5 scripts 14 exports 157 dependencies

Last updated from:6a8671c818. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	226
linux-devel-x86_64	OK	438
source / vignettes	OK	429
linux-release-x86_64	OK	438
macos-release-arm64	OK	227
macos-oldrel-arm64	OK	289
windows-devel	OK	366
windows-release	OK	415
windows-oldrel	OK	328
wasm-release	OK	250

Exports:eruption getPathwayDistances pathnetCreate pathnetFoundation pathnetGGraph pathnetVisNetwork pathwayEnrichment pathwayPlots plotFoldChange ppiBuildNetwork ppiCleanNetwork ppiEnrichNetwork ppiExtractSubnetwork ppiPlotNetwork

Dependencies:aisdk AnnotationDbi ape aplot askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem callr circlize cli clue cluster clusterProfiler codetools colorspace ComplexHeatmap cowplot cpp11 crayon curl data.table DBI digest doParallel DOSE dplyr enrichit enrichplot evaluate farver fastmap fastmatch fgsea fontawesome fontBitstreamVera fontLiberation fontquiver foreach formatR fs futile.logger futile.options gdtools generics GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree GlobalOptions glue GO.db GOSemSim graphlayouts gridExtra gridGraphics gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime nlme openssl otel patchwork permute pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rjson rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo shape sigora slam snow stringi stringr sys systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs vegan viridis viridisLite visNetwork withr xfun XVector yaml yulab.utils

Analyze and visualize RNA-Seq data with pathlinkR

Rendered frompathlinkR.Rmdusingknitr::rmarkdown

Last update: 2025-12-31
Started: 2023-10-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
INTERNAL Create manual breaks/labels for volcano plots	.eruptionBreaks
INTERNAL Construct heatmap legend	.plotFoldChangeLegend
INTERNAL Wrapper around Sigora's enrichment function	.runSigora
INTERNAL Break long strings at spaces	.truncNeatly
Create a volcano plot of RNA-Seq results	eruption
List of example results from DESeq2	exampleDESeqResults
Calculate pairwise distances from a table of pathways and genes	getPathwayDistances
Colour assignments for grouped pathways	groupedPathwayColours
Table of Hallmark gene sets and their genes	hallmarkDatabase
InnateDB PPI data	innateDbPPI
Table of KEGG pathways and genes	keggDatabase
Table of human gene ID mappings	mappingFile
Create a pathway network from enrichment results and a pathway interaction foundation	pathnetCreate
Create the foundation for pathway networks using pathway distances	pathnetFoundation
Visualize enriched Reactome pathways as a static network	pathnetGGraph
Visualize enriched Reactome pathways as an interactive network	pathnetVisNetwork
Top-level pathway categories	pathwayCategories
Test significant DE genes for enriched pathways	pathwayEnrichment
Plot pathway enrichment results	pathwayPlots
Create a heatmap of fold changes to visualize RNA-Seq results	plotFoldChange
Construct a PPI network from input genes and InnateDB's database	ppiBuildNetwork
Clean GraphML or JSON input	ppiCleanNetwork
Test a PPI network for enriched pathways	ppiEnrichNetwork
Extract a subnetwork based on pathway genes	ppiExtractSubnetwork
Plot an undirected PPI network using ggraph	ppiPlotNetwork
INTERNAL Find and return the largest subnetwork	ppiRemoveSubnetworks
Table of all Reactome pathways and genes	reactomeDatabase
Table of all Sigora pathways and their constituent genes	sigoraDatabase
Sigora enrichment example	sigoraExamples