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| Annotate | Annotation of segmented regions and generation of an HTML QC report |
| Annotate.ff | Annotation of segmented regions and generation of an HTML QC report, from a RDS file. |
| Annotate.ff.Batch | Runs Annotate.ff in batch mode with multithreading |
| ASCN.ASCAT | Allele-Specific Copy Number estimation using ASCAT |
| ASCN.FACETS | Allele-Specific Copy Number estimation using FACETS |
| ASCN.ff | Allele-Specific Copy Number estimation, from a RDS file. |
| ASCN.ff.Batch | Allele-Specific Copy Number estimation, from RDS files in batch mode, with multithreading. |
| ASCN.SEQUENZA | Allele-Specific Copy Number estimation using SEQUENZA |
| BINpack.Maker | Generates a "BINpack" containing binned data and GC tracks from a capture BED file for WES data. |
| CS.Process | Normalize CytoScanHD_Array arrays using Affymetrix Power Tools (APT) |
| CS.Process.Batch | Run CS.Process() in batch mode with multithreading |
| EaCoN.BedCheck | Performs checks un cleanups on a WES capture bed file |
| EaCoN.BedGC.chr | Compute GC-content of genomic regions defined by a BED file using chromosomic FASTA files. |
| EaCoN.BedGC.fasta | Compute GC-content of genomic regions defined by a BED file using a single genomic FASTA file. |
| EaCoN.set.bitmapType | Changes the environment variable bitmapType |
| GC.data | Dataset containing GC-content data |
| gen.df | Human gene symbols and chromosomal positions (refGene) |
| OS.Process | Normalize OncoScan / OncoScan_CNV arrays using Affymetrix Power Tools (APT) |
| OS.Process.Batch | Runs OS.Process in batch mode with multithreading |
| Segment.ASCAT | L2R and BAF joint segmentation using ASCAT. |
| Segment.FACETS | L2R and BAF joint segmentation using FACETS. |
| Segment.ff | L2R and BAF joint segmentation, from a RDS file. |
| Segment.ff.Batch | L2R and BAF joint segmentation, from a RDS file in batch mode, with multithreading. |
| Segment.SEQUENZA | L2R and BAF joint segmentation using SEQUENZA. |
| SNP6.Process | Normalize GenomeWideSNP_6 arrays using Affymetrix Power Tools (APT) |
| SNP6.Process.Batch | Run SNP6.Process() in batch mode with multithreading |
| targetlist | A restricted list of human gene symbols |
| WES.Bin | Computes the read depth of a pair of BAM files and bins it. |
| WES.Bin.Batch | Run WES.Bin() in batch mode with multithreading |
| WES.Normalize | Normalization of binned WES data. |
| WES.Normalize.ff | Normalization of binned WES data from a RDS file. |
| WES.Normalize.ff.Batch | Normalization of binned WES data from a RDS file in batch mode, with multithreading. |