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:Wei Jiang

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'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

35 exports 1 stars 0.36 score 78 dependencies 1 dependents 3 scripts 223 downloads

Last updated 7 years agofrom:a5c1c4273b. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-linuxOKSep 13 2024

Exports:AUECDownloadKGMLfilterNodegetEntrygetGeneFromEnzymegetGeneFromKGenegetGeneFromKOgetGraphicsgetKGeneFromEnzymegetKGeneFromKOgetNonMetabolicGraphgetOrgAndIdTypegetPathwaygetProductgetReactiongetRelationgetSimpleGraphgetSubstrategetSubtypegetUGraphgetUnknowProductgetUnknowReactiongetUnknowRelationgetUnknowSubstrategetUnknowSubtypeimportLatesDatamapNodeNodeGeneNodeGeneDataPathNetworksimplifyGraphTPEAUPDATEViewLatestTimeviewpathway

Dependencies:backportsbitbit64bitopsbroomclicliprcodetoolscolorspacecpp11crayondplyrevaluatefansifarverforcatsforeachgeeMgeepackgenericsggformulaggplot2ggridgesglmnetgluegtablehavenhighrhmsigraphisobanditeratorskinship2knitrlabelinglabelledlatticelifecyclemagrittrMASSMatrixMESSmgcvmosaicCoremunsellmvtnormnlmepillarpkgconfigprettyunitsprogresspurrrquadprogR6RColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrrlangscalesshapestringistringrsurvivaltibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxfunXMLyaml

Readme and manuals

Help Manual

Help pageTopics
TPEA: A Novel Pathway enrichment analysis approach based on topological structure and updated annotation of pathwayTPEA-package
All human protein coding genesall_genes
Calculate the area under the cumulative enrichment curve (AUEC) based on the interested gene set.AUEC
Download the latest KGML filesDownloadKGML
Filter the nodes in pathwaysfilterNode
The relationship of genes and ECgene2ec
The relationship of genes and KOgene2ko
Obtain the nodesgetEntry
Obtain the genes from enzymesgetGeneFromEnzyme
Obtain the genes from KGenesgetGeneFromKGene
Obtain the genes from KOgetGeneFromKO
Recontructe the network based on pathwaysgetGraphics
Obtain genes from KGnenesgetKGeneFromEnzyme
Obtain the genes from KOgetKGeneFromKO
Convert the non-metaboloc pathway to networkgetNonMetabolicGraph
Get the type names of nodesgetOrgAndIdType
Get the pathway from KEGG database.getPathway
Get the productsgetProduct
Get the reaction of nodes in pathwaysgetReaction
Get the relation of nodes in pathwaysgetRelation
Obtain the graph of pathwaysgetSimpleGraph
Obtain the information about nodes in KEGG databasegetSubstrate
Get the type of nodesgetSubtype
Obtain the graph of pathwaysgetUGraph
Get the productsgetUnknowProduct
Get the reaction of nodes in pathwaysgetUnknowReaction
Get the relation of nodes in pathwaysgetUnknowRelation
Obtain the information about nodes in KEGG databasegetUnknowSubstrate
Obtain the types of genes in pathwaysgetUnknowSubtype
Import the latest relationship information.importLatesData
KeggGene to geneskeggGene2gene
Obtain the relationship of nodes and genesmapNode
The relationship between nodes and genesnode_gene
Restract the relationship between nodes and genes.NodeGene
Intergate list of node,gene and the score of node.NodeGeneData
The score of each node in a certain pathwaynum_node_gene_score
Reconstruct pathways to networksPathNetwork
Pathway names in KEGG Databasepathway_names
Recontructe the network based on pathwayssimplifyGraph
Statistical test and calculate the significanceTPEA
Update the latest data from KEGG databaseUPDATE
Check up the latest date of KGML filesViewLatestTime
The visualization of interested pathway based on the genes you input, such as differentially expressed genes.viewpathway