Package: pathlinkR 1.99.42

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_1.99.42.tar.gz
pathlinkR_1.99.42.zip(r-4.7-any)pathlinkR_1.99.42.zip(r-4.6-any)pathlinkR_1.99.42.zip(r-4.5-any)
pathlinkR_1.99.42.tgz(r-4.6-any)pathlinkR_1.99.42.tgz(r-4.5-any)
pathlinkR_1.99.42.tar.gz(r-4.7-any)pathlinkR_1.99.42.tar.gz(r-4.6-any)
pathlinkR_1.99.42.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:

exampleDESeqResultsHS - List of example results from DESeq2 for human
exampleDESeqResultsMM - List of example results from DESeq2 in mice
groupedPathwayColours - Colour assignments for grouped pathways
hallmarkDatabaseHS - Table of Hallmark gene sets and their genes
innateDbPPIHS - InnateDB PPI data for humans
innateDbPPIMM - InnateDB PPI data for mice
keggDatabaseHS - Table of KEGG pathways and genes in humans
keggDatabaseMM - Table of KEGG pathways and genes in mice
mappingFileHS - Table of human gene ID mappings
mappingFileMM - Table of mouse gene ID mappings
pathwayCategoriesHS - Top-level pathway categories for human
pathwayCategoriesMM - Top-level pathway categories for mouse
reactomeDatabaseHS - Table of all Reactome pathways and genes for humans
reactomeDatabaseMM - Table of all Reactome pathways and genes for mice
sigoraDatabaseHS - Table of all Sigora pathways and their constituent genes for humans
sigoraDatabaseMM - Table of all Sigora pathways and their constituent genes for mice
sigoraExamplesHS - Sigora enrichment example
sigoraExamplesMM - Sigora enrichment example in mice

On BioConductor:pathlinkR-1.9.6(bioc 3.24)pathlinkR-1.8.0(bioc 3.23)

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

6.65 score 34 stars 6 scripts 357 downloads 14 exports 158 dependencies

Last updated from:392f330295. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	204
linux-devel	OK	527
source / vignettes	OK	439
linux-release	OK	491
macos-release	OK	387
macos-oldrel	OK	253
windows-devel	OK	376
windows-release	OK	340
windows-oldrel	OK	356
wasm-release	OK	230

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

Dependencies:aisdk AnnotationDbi ape aplot askpass base64enc BH Biobase BiocBaseUtils 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: 2026-08-25
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 for human	exampleDESeqResultsHS
List of example results from DESeq2 in mice	exampleDESeqResultsMM
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	hallmarkDatabaseHS
InnateDB PPI data for humans	innateDbPPIHS
InnateDB PPI data for mice	innateDbPPIMM
Table of KEGG pathways and genes in humans	keggDatabaseHS
Table of KEGG pathways and genes in mice	keggDatabaseMM
Table of human gene ID mappings	mappingFileHS
Table of mouse gene ID mappings	mappingFileMM
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 for human	pathwayCategoriesHS
Top-level pathway categories for mouse	pathwayCategoriesMM
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 for humans	reactomeDatabaseHS
Table of all Reactome pathways and genes for mice	reactomeDatabaseMM
Table of all Sigora pathways and their constituent genes for humans	sigoraDatabaseHS
Table of all Sigora pathways and their constituent genes for mice	sigoraDatabaseMM
Sigora enrichment example	sigoraExamplesHS
Sigora enrichment example in mice	sigoraExamplesMM