TPEA-package |
TPEA: A Novel Pathway enrichment analysis approach based on topological structure and updated annotation of pathway |
all_genes |
All human protein coding genes |
AUEC |
Calculate the area under the cumulative enrichment curve (AUEC) based on the interested gene set. |
DownloadKGML |
Download the latest KGML files |
filterNode |
Filter the nodes in pathways |
gene2ec |
The relationship of genes and EC |
gene2ko |
The relationship of genes and KO |
getEntry |
Obtain the nodes |
getGeneFromEnzyme |
Obtain the genes from enzymes |
getGeneFromKGene |
Obtain the genes from KGenes |
getGeneFromKO |
Obtain the genes from KO |
getGraphics |
Recontructe the network based on pathways |
getKGeneFromEnzyme |
Obtain genes from KGnenes |
getKGeneFromKO |
Obtain the genes from KO |
getNonMetabolicGraph |
Convert the non-metaboloc pathway to network |
getOrgAndIdType |
Get the type names of nodes |
getPathway |
Get the pathway from KEGG database. |
getProduct |
Get the products |
getReaction |
Get the reaction of nodes in pathways |
getRelation |
Get the relation of nodes in pathways |
getSimpleGraph |
Obtain the graph of pathways |
getSubstrate |
Obtain the information about nodes in KEGG database |
getSubtype |
Get the type of nodes |
getUGraph |
Obtain the graph of pathways |
getUnknowProduct |
Get the products |
getUnknowReaction |
Get the reaction of nodes in pathways |
getUnknowRelation |
Get the relation of nodes in pathways |
getUnknowSubstrate |
Obtain the information about nodes in KEGG database |
getUnknowSubtype |
Obtain the types of genes in pathways |
importLatesData |
Import the latest relationship information. |
keggGene2gene |
KeggGene to genes |
mapNode |
Obtain the relationship of nodes and genes |
NodeGene |
Restract the relationship between nodes and genes. |
NodeGeneData |
Intergate list of node,gene and the score of node. |
node_gene |
The relationship between nodes and genes |
num_node_gene_score |
The score of each node in a certain pathway |
PathNetwork |
Reconstruct pathways to networks |
pathway_names |
Pathway names in KEGG Database |
simplifyGraph |
Recontructe the network based on pathways |
TPEA |
Statistical test and calculate the significance |
UPDATE |
Update the latest data from KEGG database |
ViewLatestTime |
Check up the latest date of KGML files |
viewpathway |
The visualization of interested pathway based on the genes you input, such as differentially expressed genes. |