Table 2 Known implementation of the methods provided in ToPASeq
From: ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Method | Language | Source | Pathways | Format | Input data | Methods | Issusses |
|---|---|---|---|---|---|---|---|
topologyGSA | R | Bioconductor | one example | graphNEL | GEDM | topologyGSA | too computationaly intense |
clipper | R | Bioconductor | imported from graphite | pathway | GEDM | clipper | two separate steps necessary |
DEGraph | R | Bioconductor | parsing function for KGML | graphNEL | GEDM | DEGraph | Â |
SPIA | R | Bioconductor | parsing function for KGML, H. sapiens and M. musculus pre-parsed | list of adjacency matrices | DEG and log fold-changes | SPIA | Only for EntrezGene IDs |
PRS tool | MATLAB | web a | KEGG | unknown | GEDM | PRS | can not add or modify pathways, the data must have manufacturer probeset IDs, limited set of: possible platforms, DE tests, |
PWEA | C++ | web b | human pathways from KEGG | unknown | GSD | PWEA | only for UNIX-like |
TAPPA | Java | web c | KEGG or PPI added to a gene set | - | - | TAPPA | not available |
graphite | R | Bioconductor | pathways for 14 species from up to 6 databases | Pathway | depends on the method | topologyGSA, clipper, SPIA, DEGraph, | suboptimal import of the methods |