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Table 1 Methods included in the package

From: ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data

Method Ref. Type a Hypothesis A/I b Primary Graph Implementation Input data c
TopologyGSA [14] M self-contained No DAG adjusted GEDM
DEGraph [16] M self-contained Yes DAG adjusted GEDM
clipper [15] M self-contained No DAG adjusted GEDM
SPIA [17], U competitive Yes directed adjusted DEG and their log fold-change
  [25]       
PRS [26] U competitive No directed de novo DEG and their log-fold change
PWEA [27] U competitve No undirected de novo gene-level statistics
TAPPA [8] U self-contained No undirected de novo GEDM
  1. a - M - multivariable, U - univariable b - A - Activation, I - Inhibition c - the data related to the pathway topology