Metadata-Version: 2.1
Name: sigproSS
Version: 0.0.0.27
Summary:  Decomposes mutational catalogues to mutational signatures
Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
Author: S Mishu Ashiqul Islam
Author-email: m0islam@ucsd.edu
License: UCSD
Description: # SigProfilerSingleSample
        SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator, SigProfilerExtractor and SigProfilerPlotting. 
        
        ## INSTALLATION
        In the commandline, please type the following line:
        ```
        $pip install sigproSS
        ```
        Install your desired reference genome from the command line/terminal as follows (available reference genomes are: GRCh37, GRCh38, mm9, and mm10):
        ```
        $ python
        >> from SigProfilerMatrixGenerator import install as genInstall
        >> genInstall.install('GRCh37')
        ```
        This will install the human 37 assembly as a reference genome. You may install as many genomes as you wish.
        
        open a python interpreter and import the SigProfilerExtractor module. Please see the examples of the functions. 
        
        ## FUNCTIONS
        
        ### importdata 
            
            
            Imports the path of example data.
            
            importdata()
        
            Example: 
            -------
            >>> from sigproSS import spss 
            >>> data = spss.importdata()
            This "data" variable can be used as a parameter of the first argument of the sigproSS function.
            
            To get help on the parameters and outputs of the "importdata" function, please write down the following line:
            
            >>> help(spss.importdata)
            
        ### single_sample
        
            Decompose the query samples into the global signatures.
            
            single_sample(vcf, outputdir, exome=False)
            
            Example: 
            -------
            >>> from sigproSS import spss 
            >>> data = spss.importdata()
            >>> spss.single_sample(data, "results", ref="GRCh37", exome=False)
            
            To get help on the parameters and outputs of the "importdata" function, please write down the following line:
            
            >>> help(spss.single_sample)
        ## COPYRIGHT
        This software and its documentation are copyright 2018 as a part of the sigProfiler project. The SigProfilerExtractor framework is free software and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
        
        ## CONTACT INFORMATION
        Please address any queries or bug reports to S M Ashiqul Islam (Mishu) at m0islam.ucsd.edu
        
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