| aaVariation | get the functional consequencece of SNVs located in coding region | 
| Bed2Range | Generate a GRanges objects from BED file. | 
| 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 | 
| 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 | 
| Outputaberrant | generate FASTA file containing short INDEL | 
| OutputNovelJun | generate peptide FASTA file that contains novel junctions. | 
| 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. | 
| 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 | 
| 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. |