Package: TPEA 3.1.0
Wei Jiang
TPEA: A Novel Topology-Based Pathway Enrichment Analysis Approach
We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database. We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.
Authors:
TPEA_3.1.0.tar.gz
TPEA_3.1.0.tar.gz(r-4.5-noble)TPEA_3.1.0.tar.gz(r-4.4-noble)
TPEA_3.1.0.tgz(r-4.4-emscripten)TPEA_3.1.0.tgz(r-4.3-emscripten)
TPEA.pdf |TPEA.html✨
TPEA/json (API)
# Install 'TPEA' in R: |
install.packages('TPEA', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- all_genes - All human protein coding genes
- gene2ec - The relationship of genes and EC
- gene2ko - The relationship of genes and KO
- keggGene2gene - KeggGene to genes
- node_gene - The relationship between nodes and genes
- num_node_gene_score - The score of each node in a certain pathway
- pathway_names - Pathway names in KEGG Database
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 years agofrom:a5c1c4273b. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 12 2024 |
R-4.5-linux | OK | Dec 12 2024 |
Exports:AUECDownloadKGMLfilterNodegetEntrygetGeneFromEnzymegetGeneFromKGenegetGeneFromKOgetGraphicsgetKGeneFromEnzymegetKGeneFromKOgetNonMetabolicGraphgetOrgAndIdTypegetPathwaygetProductgetReactiongetRelationgetSimpleGraphgetSubstrategetSubtypegetUGraphgetUnknowProductgetUnknowReactiongetUnknowRelationgetUnknowSubstrategetUnknowSubtypeimportLatesDatamapNodeNodeGeneNodeGeneDataPathNetworksimplifyGraphTPEAUPDATEViewLatestTimeviewpathway
Dependencies:backportsbitbit64bitopsbroomclicliprcodetoolscolorspacecpp11crayondplyrevaluatefansifarverforcatsforeachgeeMgeepackgenericsggformulaggplot2ggridgesglmnetgluegtablehavenhighrhmsigraphisobanditeratorskinship2knitrlabelinglabelledlatticelifecyclemagrittrMASSMatrixMESSmgcvmosaicCoremunsellmvtnormnlmepillarpkgconfigprettyunitsprogresspurrrquadprogR6RColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrrlangscalesshapestringistringrsurvivaltibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxfunXMLyaml