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• BioPAX parsing
  Many biological pathway resourced provide their data in the BioPAX format (http://www.biopax.org/...
• KEGG pathway heat map
  I am trying to get a KEGG pathway heat map with this python script https://github.com/ajmazurie/c...
• How to quikly know whether two genes are in the same pathway or not?
  Dear list, Is there some packages can quikly know whether two genes are in the same pathway or no...
• retrieve kegg pathway abundances from gage analysis
  Hi! I used gage in order to perform a pathway enrichment analysis, using a table with KO numbers...
• KEGG REST: retrieving genes
  Hi, I am exploring the package KEGG REST. I would like to retrieve the genes that belong to a spe...
• KEGG pathway analysis with ReportingTools
  Dear All, I am successfully using the ReportingTools package to detect over- expressed categorie...
• Gene Symbol to KEGG Pathway
  An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.et...
• Retrieving all entrez identifiers that are annotated in KEGG pathways
  Dear all, Is there any way to get all entrez identifiers that are annotated with KEGG pathways?...
• Mapping KEGG pathway names to IDs using KEGG.db package
  Hi, I am trying to convert a list of KEGG pathway name to corresponding KEGG IDs. To do that, I...
• Mapping KEGG pathway to GO term ID for Illumina gene expression data
  Hi list, Is there a way to map KEGG pathway to GO ID? Or directly, mapping KEGG pathway to Illum...
• KEGGgraph bug
  I have found a problem with how 'getKGMLurl' constructs the URL for retrieving the KGML files. It...
• DESeq2 function in interpreting the differential expression results in terms of higher order biological processes or molecular pathways
  Hi,   Does DESeq2 have a build in function for pathway analysis like Gene Ontology (GO) and KEG...
• KEGGgraph: retrieveKGML error (due to wrong ftp path)
  Dear BioC developers, as I try to use the retrieveKGML function of the KEGGgraph package, I end ...
• SPIA package with updated KEGG pathways
  Hello, KEGG pathways were recently updated. How can I use the SPIA package with the updated KEGG...
• KEGGgraph question
  Hi David, I have been using the KEGGgraph package to plot Kegg pathways. I am working on the g...
• linking metabolites to pathway (KEGG)
  Hi Group, I wanted to know if there are functions or packages in BioC that links the metabolites ...
• Pathway Analyis for C-difficile microarrays
  Hello! I am working on a data set using C-difficile two-color microarrays and would like to do s...
• Packages for GO and KEGG analysis on RNAseq data
  Dear all, We are two biologists (so very new in bioinformatic field...) working with RNAseq data...
• retrieve human readable gene names from KEGG identifiers
  Dear Dr. Zhang, I am starting to use your package KEGGgraph and I've got to a point where I cann...