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A Python package for calculating tissue-specificity metrics for gene expression.

Project description

tspex

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 popular data analysis libraries, such as NumPy, SciPy, and pandas.
  • Visualization functions.
  • Support for Jupyter notebooks.

Documentation

A complete documentation for tspex can be found at https://apcamargo.github.io/tspex/.

Installation

There are two ways to install tspex:

  • Using pip:
pip install tspex
  • Using conda:
conda install -c bioconda tspex

Python API tutorial

For a detailed guide on how to use the Python API, please check the Jupyter notebook tutorial.

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, CSV or Excel
                        formats.
  output_file           Output TSV file containing tissue-specificity values.
  method                Tissue-specificity metric. Allowed values are:
                        "counts", "tau", "gini", "simpson",
                        "shannon_specificity", "roku_specificity", "tsi",
                        "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

Project details


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