Table 1.

Module-based differential co-expression methods

Method	Module comparison	Module definition	Number of conditions	Citation	Availability
DICER	Between	De novo	Multiple	[28]	jar file available from [29], dcanr v1.0.0 R/Bioconductor package
GSCA	Within	Known	Multiple	[30]	R package available from [31]
GSNCA	Within	Known	Two	[32]	GSAR v1.18.0 R/Bioconductor package
CoGA	Within	Known	Two	[33]	R package available from [34]
DiffCoEx	Both	De novo	Multiple	[35]	dcanr v1.0.0 R/Bioconductor package
CoXpress	Within	De novo	Two	[36]	R package available from [37]
dCoxS	Within	Known	Two	[38]	Supplementary material of the original publication
DCIM	Between	De novo	De novo	[39]	R package available from [40]
DiffCorr	Between	Known	Two	[41]	DiffCorr v0.4.1 R package available from CRAN