Package: leapR 1.1.0
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:
leapR_1.1.0.tar.gz
leapR_1.1.0.zip(r-4.7)leapR_1.1.0.zip(r-4.6)leapR_1.1.0.zip(r-4.5)
leapR_1.1.0.tgz(r-4.6-any)leapR_1.1.0.tgz(r-4.5-any)
leapR_1.1.0.tar.gz(r-4.7-any)leapR_1.1.0.tar.gz(r-4.6-any)
leapR_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
leapR/json (API)
NEWS
| # Install 'leapR' in R: |
| install.packages('leapR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- kinasesubstrates - Kinase substrate lists
- krbpaths - KEGG, Reactome, BioCarta Pathways
- longlist - Long list of patient samples
- ncipid - NCI Gene lists
- shortlist - A list of pathways and genes that comprise these pathways from msigdb
On BioConductor:leapR-1.1.0(bioc 3.24)leapR-1.0.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
genesetenrichmentproteomicspathwaysgeneexpressiontranscriptomics
Last updated from:ea5f96960b. Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 177 | ||
| linux-devel-x86_64 | NOTE | 355 | ||
| source / vignettes | OK | 758 | ||
| linux-release-x86_64 | NOTE | 349 | ||
| macos-release-arm64 | NOTE | 238 | ||
| macos-oldrel-arm64 | NOTE | 208 | ||
| windows-devel | ERROR | 218 | ||
| windows-release | ERROR | 181 | ||
| windows-oldrel | ERROR | 174 | ||
| wasm-release | OK | 131 |
Exports:calcTTestcluster_enrichmentcombine_omicsget_pathway_informationleapRplot_leapr_barread_gene_sets
Dependencies:abindbase64encBiobaseBiocGenericsBiocManagerBiocStylebitbit64bitopsbookdownbslibcachemcaToolsclicliprcpp11crayonDelayedArraydigestdplyrevaluatefarverfastmapfontawesomefsgenericsGenomicRangesggplot2gluegplotsgtablegtoolshighrhmshtmltoolsIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimepillarpkgconfigprettyunitsprogresspurrrR6rappdirsRColorBrewerreadrrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXVectoryaml
leapR Paper Examples
Rendered fromexamples.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-02-06
Started: 2026-02-06
leapR
Rendered fromleapR.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-02-06
Started: 2022-01-19
leapR Order Enrichment Tests
Rendered fromorder-enrichment.Rmdusingknitr::rmarkdownon May 30 2026.Last update: 2026-02-11
Started: 2026-02-11
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calcTTest | calcTTest |
| cluster_enrichment | cluster_enrichment |
| combine_omics Combine two or more omics matrices into one multi-omics matrix with 'tagged' ids. | combine_omics |
| correlation_comparison_enrichment | correlation_comparison_enrichment |
| correlation_enrichment | correlation_enrichment |
| enrichment_in_abundance | enrichment_in_abundance |
| enrichment_in_groups | enrichment_in_groups |
| enrichment_in_relationships | enrichment_in_relationships |
| get_pathway_information | get_pathway_information |
| Kinase substrate lists | kinasesubstrates |
| KEGG, Reactome, BioCarta Pathways | krbpaths |
| leapR | leapR |
| Long list of patient samples | longlist |
| NCI Gene lists | ncipid |
| Plot leapR pathway bars (single panel) | plot_leapr_bar |
| read_gene_sets | read_gene_sets |
| A list of pathways and genes that comprise these pathways from msigdb | shortlist |
