Metadata-Version: 2.1
Name: tspex
Version: 0.4.0
Summary: A Python package for calculating tissue-specificity metrics for gene expression.
Home-page: https://github.com/apcamargo/tspex
Author: Antonio Pedro Camargo
Author-email: antoniop.camargo@gmail.com
License: GNU General Public License v3.0
Description: # tspex
        
        - [Overview](#overview)
        - [Installation](#installation)
        - [Python API tutorial](#python-api-tutorial)
        - [Command-line interface](#command-line-interface)
        - [Examples](#examples)
        
        ## Overview
        
        tspex is a tissue-specificity calculator tool. It provides both an easy-to-use object-oriented Python API and a command-line interface (CLI) for calculating a variety of tissue-specificity metrics from gene expression data.
        
        tspex features include:
          - Twelve different tissue-specificity metrics.
          - Integration with pandas.
          - Visualization functions.
          - Support for Jupyter notebooks.
        
        ## Installation
        
        1. Using pip:
        
        ```
        $ pip install rnasamba
        ```
        
        2. Using conda:
        
        ```
        $ conda install -c bioconda rnasamba
        ```
        
        
        ## Python API tutorial
        
        For a detailed guide on how to use the Python API, please check the [Jupyter notebook tutorial](https://github.com/apcamargo/tspex/blob/master/tutorial.ipynb).
        
        
        ## Command-line interface
        
        tspex can be executed from the command line using the `tspex` command. It takes an expression matrix file as input and outputs the computed tissue-specificity values.
        
        
        ```
        usage: tspex [-h] [-l] [-d] [-t THRESHOLD] input_file output_file method
        
        Compute gene tissue-specificity from an expression matrix and save the output.
        
        positional arguments:
          input_file            Expression matrix file in the TSV or CSV formats.
          output_file           Output TSV file containing tissue-specificity values.
          method                Tissue-specificity metric. Allowed values are:
                                "counts", "tsi", "tau", "gini", "simpson",
                                "shannon_specificity", "roku_specificity", "zscore",
                                "spm", "spm_dpm", "js_specificity",
                                "js_specificity_dpm".
        
        optional arguments:
          -h, --help            show this help message and exit
          -l, --log             Log-transform expression values. (default: False)
          -d, --disable_transformation
                                By default, tissue-specificity values are transformed
                                so that they range from 0 (perfectly ubiquitous) to 1
                                (perfectly tissue-specific). If this parameter is
                                used, transformation will be disabled and each metric
                                will have have a diferent range of possible values.
                                (default: False)
          -t THRESHOLD, --threshold THRESHOLD
                                Threshold to be used with the "counts" metric. If
                                another method is chosen, this parameter will be
                                ignored. (default: 0)
        ```
        
        ### Examples
        
        - Using the `spm` metric to compute tissue-specificity values from a log-transformed expression matrix:
        
        ```
        tspex --log gene_expression.tsv tspex_spm.tsv spm
        ```
        
        - Using the `counts` method to compute tissue-specificity by counting the number of tissues in which the gene expression is greater than 10:
        
        ```
        tspex --threshold 10 gene_expression.tsv tspex_counts.tsv counts
        ```
        
        - Using the `zscore` without transformation to quantify tissue-specificity as the number of standard deviations away from the mean gene expression:
        
        ```
        tspex --disable_transformation gene_expression.tsv tspex_zscore.tsv zscore
        ```
        
Keywords: bioinformatics,gene expression,tissue-specificity,transcriptomics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3
Description-Content-Type: text/markdown
