From: A comparative study of topology-based pathway enrichment analysis methods
Method | Null hypothesis | Gene p-value thresholding | Expression data | Pathway | R/Bioconductor | Reference |
---|---|---|---|---|---|---|
Pathway-Express | Competitive | Optional | No | Topology | ROntoTools 2.10.0 | [8] |
SPIA | Competitive | Yes | No | Topology | graphite 1.28.2 | [9] |
NetGSA | Self-contained | No | Yes | Topology | netgsa 3.1.0 | |
topologyGSA | Self-contained | No | Yes | Topology | topologyGSA 1.4.6 | [12] |
DEGraph | Self-contained | No | Yes | Topology | DEGraph 1.34.0 | [13] |
CAMERA | Competitive | No | Yes | Membership | limma 3.38.3 | [14] |
CePa | Competitive | Yes | No | Topology | CePa 0.6 | |
PRS | Competitive | Yes | No | Topology | ToPASeq 1.16.1 | |
PathNet | Competitive | Yes | No | Topology | PathNet 1.22.0 | [17] |