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 |