Table 1.

Methods included in the package

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

^a - M - multivariable, U - univariable ^b - A - Activation, I - Inhibition ^c - the data related to the pathway topology