ASCN.ASCAT              Allele-Specific Copy Number estimation using
                        ASCAT
ASCN.FACETS             Allele-Specific Copy Number estimation using
                        FACETS
ASCN.SEQUENZA           Allele-Specific Copy Number estimation using
                        SEQUENZA
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.
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
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
OS.Process              Normalize OncoScan / OncoScan_CNV arrays using
                        Affymetrix Power Tools (APT)
OS.Process.Batch        Runs OS.Process in batch mode with
                        multithreading
SNP6.Process            Normalize GenomeWideSNP_6 arrays using
                        Affymetrix Power Tools (APT)
SNP6.Process.Batch      Run SNP6.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.SEQUENZA        L2R and BAF joint segmentation using SEQUENZA.
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.
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.
gen.df                  Human gene symbols and chromosomal positions
                        (refGene)
targetlist              A restricted list of human gene symbols
