search for: pathview

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, species = "h...

...erforms pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways. pathfindR also creates pathway diagrams with the involved genes colored by change values. (this is achieved using the bioconductor package pathview) Finally, the package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and reduces the complexity of analysis. You can read more about the package and a case study in our pre-print <https://doi.org/10.1101/272450> [[...

...erforms pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways. pathfindR also creates pathway diagrams with the involved genes colored by change values. (this is achieved using the bioconductor package pathview) Finally, the package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and reduces the complexity of analysis. You can read more about the package and a case study in our pre-print <https://doi.org/10.1101/272450> [[...