Table 2.
Network-based differential co-expression analysis methods
| Method | Statistical method | Test | Number of conditions | Citation | Availability |
|---|---|---|---|---|---|
| z-score | Correlation | z-test | Two | [43] | dcanr v1.0.0 R/Bioconductor package |
| DGCA | Correlation | z-test | Two | [9] | DGCA v1.0.1 R package available from CRAN |
| Discordant | Correlation | z-test | Two | [10] | discordant v1.8.0 R/Bioconductor package |
| MAGIC | Correlation | Modulation test | Two | [11] | dcanr v1.0.0 R/Bioconductor package |
| DICER | Correlation | Permutation test | Multiple | [28] | jar file available from [29], dcanr v1.0.0 R/Bioconductor package |
| DiffCoEx | Correlation | Permutation test | Multiple | [35] | dcanr v1.0.0 R/Bioconductor package |
| EBcoexpress | Empirical Bayes + correlation | – | Two | [7] | EBcoexpress v1.28.0 R/Bioconductor package |
| Entropy (ENT) | Entropy based on correlation | Permutation test | Two | [44] | dcanr v1.0.0 R/Bioconductor package |
| FTGI | Generalised linear model | Chi-squared test | Multiple | [45] | dcanr v1.0.0 R/Bioconductor package |
| ECF | Expected conditional F | Permutation test | Multiple | [46] | COSINE v2.1 R package available from CRAN |
| COSINE | Expected conditional F | – | Multiple | [8] | COSINE v2.1 R package available from CRAN |
| GGM-based | GGM + posterior odds | – | Two | [47] | dcanr v1.0.0 R/Bioconductor package |
| LDGM | Latent differential graphical model | – | Two | [48] | dcanr v1.1.4 R/Bioconductor package |
| MINDy | Conditional mutual information | Permutation test | Two | [49] | MINDy module in GenePattern, dcanr v1.0.0 R/Bioconductor package |