Metadata-Version: 2.1
Name: oncoboxlib
Version: 1.2.2
Summary: Oncobox collections of libraries
Home-page: https://gitlab.com/oncobox/oncoboxlib
Author: Alexander Simonov <registsys@mail.ru>, Victor Tkachev <victor.tkachev@yandex.com>
Author-email: tkachev@oncobox.com
License: LICENSE.txt
Description: # oncoboxlib
        
        Oncobox library calculates Pathways Activation Levels (PAL) according to
        Sorokin et al.(doi: 10.3389/fgene.2021.617059).
        It takes a file that contains gene symbols in HGNC format (see genenames.org),
        their expression levels for one or more samples (cases and/or controls)
        and calculates PAL values for each pathway in each sample.
        
        ## Installation
        
        ```
        pip install oncoboxlib
        ```
        
        ## How to run the example
        
        1. Create any directory that will be used as a sandbox. Let's assume it is named `sandbox`.
        
        
        2. Extract `resources/databases.zip` into `sandbox/databases/`.
          <br> (You may download the archive from 
          `https://gitlab.com/oncobox/oncoboxlib/-/blob/master/resources/databases.zip`)
          
        
        3. Extract example data `resources/cyramza_normalized_counts.txt.zip` into `sandbox`.
          <br> (You may download the archive from 
          `https://gitlab.com/oncobox/oncoboxlib/-/blob/master/resources/cyramza_normalized_counts.txt.zip`)
          
        
        What it looks like now:
        ```
           - sandbox
               - databases
                   - Balanced 1.123
                   - KEGG Adjusted 1.123
                   ...
               - cyramza_normalized_counts.txt  
        ```
        
        4. Change directory to `sandbox` and execute the command:
        ```
        oncoboxlib_calculate_scores --databases-dir=databases/ --samples-file=cyramza_normalized_counts.txt
        ```
        It will create a result file `sandbox\pal.csv`.
        
        
        Alternatively, you can use it as a library in your source code.
        For details please see `examples` directory.
        
        
        ## Input file format
        
        Table that contains gene expression.
        Allowed separators: comma, semicolon, tab, space.
        Compressed (zipped) files are supported as well.
        
        - First column - gene symbol in HGNC format, see genenames.org.
        - Others columns - gene expression data for cases or controls.
        - Names of case columns should contain "Case", "Tumour", or "Tumor", case insensitive.
        - Names of control columns should contain "Control" or "Norm", case insensitive.
        
        It is supposed that data is already normalized by DESeq2, quantile normalization or other methods.
        
        
        ## Help
        
        ```
        usage: calculate_scores.py [-h] --samples-file SAMPLES_FILE
                                   [--controls-file CONTROLS_FILE] [--ttest]
                                   [--fdr-bh] --databases-dir DATABASES_DIR
                                   [--databases-names DATABASES_NAMES]
                                   [--results-file RESULTS_FILE]
        
        Command line tool for calculation of pathway activation level according to
        doi: 10.3389/fgene.2021.617059
        
        optional arguments:
          -h, --help            show this help message and exit
                                
          --samples-file SAMPLES_FILE
                                Table that contains gene expression for cases (or
                                cases and controls). Allowed separators: comma,
                                semicolon, tab, space. Compressed (zipped) files are
                                supported as well. First column - gene symbol in HGNC
                                format, see genenames.org. Others columns - gene
                                expression data for cases or controls. Names of case
                                columns should contain "Case", "Tumour", or "Tumor",
                                case insensitive. Names of control columns should
                                contain "Control" or "Norm", case insensitive. It is
                                supposed that data is already normalized by DESeq2,
                                quantile normalization or other methods.
                                
          --controls-file CONTROLS_FILE
                                Optional file that contains controls. If provided,
                                cases and controls will be increased by one and
                                normalized by quantile normalization.
                                
          --ttest               Include to result a column for unequal variance t-test
                                two-tailed p-values (aka Welch's t-test). It is
                                assumed that cases and norms are independent. t-test
                                will be performed between all cases and all controls.
                                
          --fdr-bh              Include to result a column for p-values corrected for
                                FDR using Benjamini/Hochberg method
                                
          --databases-dir DATABASES_DIR
                                Directory that contains pathway databases. Databases
                                can be downloaded from https://gitlab.com/oncobox/onco
                                boxlib/-/blob/master/resources/databases.zip (Biocarta
                                1.123, KEGG Adjusted 1.123, Metabolism 1.123, NCI
                                1.123, Qiagen 1.123, Reactome 1.123)
                                
          --databases-names DATABASES_NAMES
                                Names of databases that are used to calculate PALs.
                                "all" means that all database from --databases-dir
                                will be used.
                                
          --results-file RESULTS_FILE
                                Output file that will contain results, "pal.csv" by
                                default
                                
        ```
        
Keywords: bioinformatics,transcriptomics,pathways
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
