batch_file              Process the input file a batch of one batch
format_filenames        Function to format filenames that can be used
                        to unify the filenames style for more easily
                        download or use
format_pp_meta_age      To format ProteinPaint input meta data of age
format_pp_meta_fusions
                        To format ProteinPaint input meta data of
                        gender
format_pp_meta_gender   To format ProteinPaint input meta data of
                        gender
fusions2oncoprinter     Function to convert fusion data to cbioportal
                        Oncoprinter format.
fusions2pp              Function to convert fusion data to ProteinPaint
                        format.
fusions2pp_meta         Function to convert fusion data to ProteinPaint
                        heatmap meta rows format.
fusions_filter          Fusions handler_data filter that can be used to
                        prepare the input data for downstream analysis
get_files_ctime         Function to check file create time and
                        according the requirement to return check value
get_files_mtime         Function to check file last change time and
                        according the requirement to return check value
get_pp_samplegroup      Function to get samplegroup file that can be
                        pass to Proteinpaint
get_split_seqs          Function to calculate the split regions by
                        sections and total numbers
make_option             Functions to enable our OptionParser to
                        recognize specific command line options
                        (optparse).
merge_table_files       Util function to merge multiple table files.
muts2mutation_mapper    Function to convert mutation data to cbioportal
                        MutationMapper format.
muts2oncoprinter        Function to convert mutation data to cbioportal
                        Oncoprinter format.
muts2pp                 Function to convert mutation data to
                        ProteinPaint format.
ngstk                   ngstk can be used to facilitate the analysis of
                        NGS data, such as visualization, conversion of
                        data format for WEB service input and other
                        purpose.
opt_parser              A function to create an instance of a parser
                        object with subcommands.
par_download            Function to download multiple file at the same
                        time.
parse_args              Parse command line options (optparse).
parse_args2             Parse command line options.
print_help              Printing an usage message from an OptionParser
                        object
rbin                    Function to generate executable files for R
                        package
set_colors              Function to get a series defined theme colors
set_tools               Function to generate tools path object
show_handlers           Function to show all avaliabe handler function
show_mhandlers          Function to show all avaliabe mhandler function
split_col_data          Data split function by colum
split_list              Function to split list
split_row_data          Data split function by row
split_row_file          Function to split big file to a series small
                        files (by row)
supress_any_message     suppressWarnings(suppressMessages(...))
time_stamp              Function to generate time stamp in the files
                        name or directories name.
