Package: leapR 1.1.2

Sara Gosline

leapR: Layered enrichment analysis of pathways R

leapR is a package that identifies pathways that are enriched across diverse 'omics experiments. It leverages any tabular expression data (proteomics, transcriptomics) using the `SummarizedExperiment` object. It works with any pathway in the .gct file format.

Authors:Sara Gosline [aut, cre], Jason McDermott [aut], Jeremy Jacobson [aut], Vincent Danna [ctb], National Institutes of Health [fnd]

leapR_1.1.2.tar.gz
leapR_1.1.2.zip(r-4.7)leapR_1.1.2.zip(r-4.6)leapR_1.1.2.zip(r-4.5)
leapR_1.1.2.tgz(r-4.6-any)leapR_1.1.2.tgz(r-4.5-any)
leapR_1.1.2.tar.gz(r-4.7-any)leapR_1.1.2.tar.gz(r-4.6-any)
leapR_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
leapR/json (API)

# Install 'leapR' in R:
install.packages('leapR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pnnl/leapr/issues

Pkgdown/docs site:https://pnnl.github.io

Datasets:

On BioConductor:leapR-1.1.0(bioc 3.24)leapR-1.0.0(bioc 3.23)

genesetenrichmentproteomicspathwaysgeneexpressiontranscriptomicssoftware

8.28 score 19 stars 92 scripts 182 downloads 7 exports 95 dependencies

Last updated from:671d76fa86. Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING183
linux-devel-x86_64NOTE345
source / vignettesOK715
linux-release-x86_64NOTE354
macos-release-arm64NOTE259
macos-oldrel-arm64NOTE233
windows-develERROR221
windows-releaseERROR246
windows-oldrelERROR215
wasm-releaseOK136

Exports:calcTTestcluster_enrichmentcombine_omicsget_pathway_informationleapRplot_leapr_barread_gene_sets

Dependencies:abindaskpassbase64encBiobaseBiocFileCacheBiocGenericsBiocManagerBiocStylebitbit64bitopsblobbookdownbslibcachemcaToolsclicliprcpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrevaluatefarverfastmapfilelockfontawesomefsgenericsGenomicRangesggplot2gluegplotsgtablegtoolshighrhmshtmltoolshttr2IRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigprettyunitsprogresspurrrR6rappdirsRColorBrewerreadrrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXVectoryaml

leapR
Installation | Load libraries needed | Introduction | Definitions | Important points for consideration | Data normalization | Background | Multiple hypothesis correction | Pathway databases | Identifiers | Example data | Examples | Comparison of one condition/group versus another condition/group. | Caveat | Description | Interpretation | Fisher's exact test | Caveats | Visualizing Fisher's exact results | The Kolmogorov–Smirnov test (KS) | Visualizing KS test results | KS alternative: the one-sample Z test | Enrichment in Correlation | Visualizing correlation enrichment results | Phosphoproteomics data analysis | Visualizing kinase substrate enrichment
Rendered fromleapR.Rmdusingknitr::rmarkdown

Last update: 2026-06-10
Started: 2022-01-19

leapR Order Enrichment Tests
Load libraries needed | Load our test proteomics dataset | Compare enrichment methods
Rendered fromorder-enrichment.Rmdusingknitr::rmarkdown

Last update: 2026-06-10
Started: 2026-03-10

leapR Paper Examples
Load libraries needed | Example data | Figure 2
Rendered fromexamples.Rmdusingknitr::rmarkdown

Last update: 2026-03-11
Started: 2026-02-12