Package: pathlinkR 1.3.7

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_1.3.7.tar.gz
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pathlinkR_1.3.7.tgz(r-4.4-any)pathlinkR_1.1.17.tgz(r-4.3-any)
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pathlinkR.pdf |pathlinkR.html✨
pathlinkR/json (API)
NEWS

# 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-1.3.3(bioc 3.21)pathlinkR-1.2.0(bioc 3.20)

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

6.63 score 25 stars 2 scripts 168 downloads 14 exports 178 dependencies

Last updated 3 days agofrom:a80da73101. Checks:OK: 2 NOTE: 3 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 24 2024
R-4.5-win	ERROR	Dec 24 2024
R-4.5-linux	OK	Dec 24 2024
R-4.4-win	ERROR	Dec 24 2024
R-4.4-mac	NOTE	Dec 24 2024
R-4.3-win	NOTE	Sep 24 2024
R-4.3-mac	NOTE	Sep 24 2024

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

Dependencies:abind AnnotationDbi ape aplot askpass backports base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob boot broom bslib cachem car carData circlize cli clue cluster clusterProfiler codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon curl data.table DBI Deriv digest doBy doParallel DOSE dplyr enrichplot evaluate fansi farver fastmap fastmatch fgsea fontawesome foreach formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GetoptLong ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggsci ggsignif ggtangle ggtree GlobalOptions glue GO.db GOSemSim graphlayouts gridExtra gridGraphics gson gtable highr htmltools htmlwidgets httr igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle lme4 magrittr MASS Matrix MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr munsell nlme nloptr nnet numDeriv openssl patchwork pbkrtest permute pillar pkgconfig plogr plyr png polyclip polynom purrr quantreg qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rjson rlang rmarkdown RSQLite rstatix S4Vectors sass scales scatterpie shape sigora slam snow SparseM stringi stringr survival sys systemfonts tibble tidygraph tidyr tidyselect tidytree tinytex treeio tweenr UCSC.utils utf8 vctrs vegan viridis viridisLite visNetwork withr xfun XVector yaml yulab.utils

Analyze and visualize RNA-Seq data with pathlinkR

Andy An, Travis Blimkie

Rendered frompathlinkR.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-11-20
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