# A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

## Documentation for package ‘DEComplexDisease’ version 1.13.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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