Next-Generation Sequencing (NGS) Data Analysis Toolkit


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Documentation for package ‘ngstk’ version 0.2.1

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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 mutation data to Oncoprinter <URL: http://www.cbioportal.org/oncoprinter.jsp> input format.
fusions2pp Function to convert fusion data to ProteinPaint <URL: https://pecan.stjude.org/pp> input format.
fusions2pp_meta Function to convert fusion data to ProteinPaint heatmap meta rows <URL: 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 <URL: http://www.cbioportal.org/mutation_mapper.jsp> input format.
muts2oncoprinter Function to convert mutation data to Oncoprinter <URL: http://www.cbioportal.org/oncoprinter.jsp> input format.
muts2pp Function to convert mutation data to ProteinPaint <URL: 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)