Welcome

page is a Python library to perform Parametric Analysis of Gene Set Enrichment.

Head to the Installation to see installation instructions, to Usage for quick use, or have a look at the catalogue of available functions in the API.

Contents

Installation

With pip

page is available for Python 3 only. Is is tested in Python 3.6 and 3.7.

To install, simply do:

pip install page-enrichment

you might need to add a --user flag if not root or running in a virtual environment.

This will install all the Python dependencies needed too. See here a list of all Python dependencies used.

To install the latest development version:

pip install git+https://github.com/afrendeiro/page-enrichment.git#egg=page

Quick usage

Using the command-line interface (CLI)

page has a CLI for easy usage:

$ page-get-test-data test.csv
$ page -g KEGG_2016 test.csv output.csv

Interactive usage through the API

Example usage of the page.page() function:

from page import page, get_test_data

vect = get_test_data()
results = page(vect, gene_set_libraries=['KEGG_2016'])

The page.get_test_data() function serves simply the purpose of getting a vector of fold-changes to use with PAGE.

Configuration and logging

Gene set libraries and configuration

page uses gene sets from Enrichr gene set libraries.

Enrichment of a few is performed by default but this can be customizable by the user.

The user can customize page in two ways:

  • In a YAML file located in $HOME/.page.config.yaml;

  • At run time with through the gene_set_libraries option in the page.page() function.

  • At run time with the -g or --gene-set-libraries option if using the command-line interface.

The YAML configuration file is entirely optional, but does allow more flexibility and ease specically when selecting a large number of gene set libraries (each with its own gene sets).

To see which gene set libraries are available, go to https://amp.pharm.mssm.edu/Enrichr/#stats.

page does not need any static files with genes, but gets automatically what is needed and keeps a cache of what has been used in order to save API calls and greatly improve speed.

Logging

page will log its operations and errors using the Python standard logging library.

This will happen by default to standard output (sys.stdout) but also to a file in $HOME/.page.log.txt.

The location of the log file and the level of events to be reported can be customized in the page.setup_logger() function.

API

page

Parametric Analysis of Gene Set Enrichment (PAGE).

Parameters

  • parameter_vector (Series) – Pandas series with index as genes and values as ‘parameters’ (e.g. fold-changes, expression values)

  • gene_set_libraries (list, optional) – Gene set libraries to use. Defaults to values in default configuration file or in ~/.page.config.yaml. To see all available values go to https://amp.pharm.mssm.edu/Enrichr/#stats

returns

Data frame with enrichment statistics for each term in each gene set library.

rtype

DataFrame

Testing

page does not have many dependencies, but to make sure everything is correctly configured, the user is encouraged to test the library prior to use.

In order to do this, install testing requirements and simply run pytest:

pip install page-enrichment[testing]
pytest --pyargs page

Pytest will output summary results (see for example) and further outputs can be seen in ${TMPDIR}/pytest-of-${USER}/ or /tmp/pytest-of-${USER}/ if $TMPDIR is not defined.

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[0.1.0] - 2020-02-06

Added

  • Basic functionality to perform enrichmemnt, get gene sets from Enrichr and CLI

Indices and tables