| CODEX-package | A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing | 
| bambedObjDemo | Demo data pre-stored for bambedObj. | 
| choiceofK | Determine the number of latent factors K. | 
| CODEX | A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing | 
| coverageObjDemo | Demo data pre-stored for coverageObj. | 
| gcDemo | Demo data pre-stored for GC content. | 
| getbambed | Get bam file directories, sample names, and exonic positions | 
| getcoverage | Get depth of coverage from whole exome sequencing | 
| getgc | Get GC content for each exonic target | 
| getmapp | Get mappability for each exonic target | 
| mappability | Pre-computed mappabilities | 
| mappDemo | Demo data pre-stored for mappability. | 
| mapp_ref | Position reference for pre-computed mappability results. | 
| normalize | Normalization of read depth from whole exome sequencing | 
| normalize2 | Normalization of read depth from whole exome sequencing under the case-control setting | 
| normObjDemo | Demo data pre-stored for normObj. | 
| qc | Quality control procedure for depth of coverage | 
| qcObjDemo | Demo data pre-stored for qcObj. | 
| segment | Recursive segmentation algorithm for CNV detection and genotyping |