Table 2.
“Global network” methods that can also be employed for the “gene-specific” approach.
| Method | Number of Conditions | Citation | Availability |
|---|---|---|---|
| DINGO | Multiple | [40] | CRAN R package (iDINGO) |
| Entropy | Two | [41] | Bioconductor R package (dcanr) |
| DGCA | Two | [42] | CRAN R package (DGCA) |
| Discordant | Two | [43] | Bioconductor R package (Discordant) |
| MAGIC | Two | [44] | Bioconductor R package (dcanr) MATLAB implementation at https://github.com/chiuyc/MAGIC |
| EBcoexpress | Two | [45] | Bioconductor R package (EBcoexpress) |
| GGM-based | Two | [46] | Bioconductor R package (dcanr) |
| LDGM | Two | [47] | Bioconductor R package (dcanr) Matlab implementation at https://github.com/ma-compbio/LDGM |
| Gill | Two | [48] | R package at http://www.somnathdatta.org/Supp/DNA |
| DDN | Two | [49] | MATLAB toolbox at http://www.cbil.ece.vt.edu/software.htm |
| Zhao | Two | [50] | |
| JDINAC | Two | [51] | R code at https://github.com/jijiadong/JDINAC |
| TDJGL | Two | [52] | R code at https://github.com/Zhangxf-ccnu/TDJGL |
| mlDNA | Two | [53] | CRAN R package (mlDNA, not maintained) |
| DCGL | Two | [54] | CRAN R package (DCGL) |
| DECODE | Two | [55] | CRAN R package (DECODE) |
| SIG method | Two | [56] | |
| Discordant | Two | [43] | Bioconductor R package (discordant) |
| DCN | Two | [57] | R package at https://github.com/weiliu123/DCN-package |
| TCDV | Two | [58] | |
| BFDCA | Two | [59] | R package at http://dx.doi.org/10.17632/jdz4vtvnm3.1 |
| CODC | Two | [60] | R package at https://github.com/Snehalikalall/CODC |
| z-score | Two/De novo | [61] | Bioconductor R package (dcanr) |
| MINDy | De novo | [62] | Bioconductor R package (dcanr) |