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| ann.er | ER status annotation |
| bi.deg | Transformation an expression matrix to binary differential expression matrix |
| cl | Binary patient annotation (part) |
| cluster.mod | seed-based module analysis (part) |
| cluster.module | Predict the DEGs modules shared by patients |
| deg | DEG matrix of breast cancer (part) |
| deg.spc | The patient-specific DEGs (part) |
| deg.specific | Predict the patient-specific DEGs using bi-clustering analysis |
| exp | expression matrix of breast cancer (part) |
| module.compare | Compare and plot the overlap among predicted modules |
| module.curve | Display the patient-gene numbers during bi-clustering analysis |
| module.exact | Extract the patients and genes from module |
| module.extract | Extract the patients and genes from module |
| module.modeling | Predict and report the proper gene-patient number of bi-clustering analysis |
| module.overlap | Plot the overlap among predicted DEG modules |
| module.screen | Screen the feature patients or genes in predicted modules |
| Plot | Plot the DEGs before or after cross-validation |
| Plot.cluster.module | Plot the DEGs modules |
| Plot.deg | Plot the DEGs before or after cross-validation |
| Plot.deg.specific | Plot the DEGs before or after cross-validation |
| Plot.deg.specific.test | Plot the DEGs before or after cross-validation |
| Plot.seed.module | Plot the DEGs modules shared by patients |
| res.mod1 | clustered module 1 |
| res.mod2 | clustered module 1 |
| seed.mod | seed-based module analysis (part) |
| seed.module | Predict the DEGs modules shared by patients |
| summarize | Summarize the DEG modules |
| summarize.cluster.module | Summarize the DEG modules |
| summarize.deg.specific | Summarize the patient-specific DEGs |
| summarize.seed.module | Summarize the DEG modules |