Bed2Range               Generate a GRanges objects from BED file.
InputVcf                Generate a list of GRanges objects from a VCF
                        file.
JunctionType            Annotates the junctions in a bed file.
Multiple_VCF            Generate shared variation dataset from multiple
                        VCF files
OutputNovelJun          generate peptide FASTA file that contains novel
                        junctions.
OutputVarprocodingseq   Output the variant(SNVs) protein coding
                        sequences
OutputVarproseq         Output the variant(SNVs) protein sequences into
                        FASTA format
OutputVarproseq_single
                        Output the variant(SNVs) protein sequences into
                        FASTA format
Outputaberrant          generate FASTA file containing short INDEL
Outputproseq            output FASTA format file contains proteins that
                        have expression level above the cutoff
OutputsharedPro         Output the sequences of proteins with high
                        expressions in multiple samples.
Positionincoding        Find the position in coding sequence for each
                        variation.
PrepareAnnotationEnsembl
                        prepare annotation from ENSEMBL
PrepareAnnotationRefseq
                        prepare annotation for Refseq
SharedJunc              Generate shared junctions dataset from multiple
                        BED files
Varlocation             Annotates the variations with genomic location.
aaVariation             get the functional consequencece of SNVs
                        located in coding region
calculateRPKM           Caculate RPKM for each transcripts based on
                        exon read counts.
easyRun                 An integrated function to generate customized
                        protein database for a single sample
easyRun_mul             An integrated function to generate consensus
                        protein database from multiple samples
