ngstk-package |
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. |
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. |
parse_args |
Parse command line options (optparse). |
parse_args2 |
Parse command line options. |
par_download |
Function to download multiple file at the same time. |
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. |