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    Github
    https://github.com › pbagos › mage

    pbagos/mage: MAGE :: Meta-Analysis of Gene Expression - GitHub

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    pbagos/mage: MAGE :: Meta-Analysis of Gene Expres…

    MAGE (v2.0) web tool : http://rs.dib.uth.gr:3839/MAGE/

    Github

    MAGE, is an acronym for Meta-Analysis of Gene Expression.

    The overall aim of this work has been to develop a software tool that would offer a large collection of meta-analysis options, as well as several extensions to evaluate the software applied to various biological problems. The MAGE framework is characterized by: Speed: It takes a small amount of time to perform the functions which are included Effectiveness: It gives reliable estimations and results, thanks to the mathematical models which are implemented. Compatibility: It can be executed either from a Windows or a UNIX operating system.

    Also, there is no need for the user to be expert of any programming or computer science knowledge to run MAGE.

    MAGE is a Python package that can be run from the command line. MAGE is written in Python (ver. 3.7.9) and requires the following Python libraries and packages to run:

    Requirements

    •Pandas~=1.2.4

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    1.Download MAGE from: https://github.com/pbagos/mage

    Otherwise, you can run MAGE from its online infrastructure at: http://www.compgen.org/tools/mage (Mozila Firefox browser is suggested) MAGE (v2.0) web tool : http://rs.dib.uth.gr:3839/MAGE/

    2.After downloading the .zip folder of MAGE from GitHub, extract it to a working directory.

    3.Το install the requirements, pip needs to be installed. Download the script for pip, from: https://bootstrap.pypa.io/get-pip.py.

    4.Open a terminal/command prompt, cd to the folder containing the get-pip.py file and run:

    python get-pip.py

    5.To install the mentioned requirements with pip, open a terminal/command prompt and run:

    pip install -r /path/to/requirements.txt

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    MAGE provides the following command-line arguments:

    -c: The configuration (.txt) file which contains the settings selected from the user.

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    MAGE is consisted of three basic functions.

    GISU (Gene ID / Symbol update)

    MAGE uses an optional component called GISU to transform the platform's probe identifiers to gene symbols identifiers. These can be helpful when one is comparing datasets aris-ing from different platforms, then the probe identifiers must be con-verted to gene identifiers. Considering that multiple probes may corre-spond to the same gene in a microarray experiment [1], the multiple entries of the same gene can be combined into one using the minimum, maximum or arithmetic mean (average) [1,2,3]. If the experiment's platform is not included in the list, the user can upload the platform file in order to proceed to the transformation.

    Meta-analysis:

    For meta-analysis, the package supports the standard meta-analysis, bootstrap meta-analysis and multivariate meta-analysis functions.

    Enrichment analysis:

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