All functions

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 mutation data to Oncoprinter http://www.cbioportal.org/oncoprinter.jsp input format.

fusions2pp()

Function to convert fusion data to ProteinPaint https://pecan.stjude.org/pp input format.

fusions2pp_meta()

Function to convert fusion data to ProteinPaint heatmap meta rows https://pecan.stjude.org/pp input 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

merge_table_files()

Util function to merge multiple table files.

muts2mutation_mapper()

Function to convert mutation data to MutationMapper http://www.cbioportal.org/mutation_mapper.jsp input format.

muts2oncoprinter()

Function to convert mutation data to Oncoprinter http://www.cbioportal.org/oncoprinter.jsp input format.

muts2pp()

Function to convert mutation data to ProteinPaint https://pecan.stjude.org/pp input 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.

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(...))