mageck2 0.2.0

MAGeCK2: Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout screens

MAGeCK2: Model-based Analysis of CRISPR screens

MAGeCK2 is a new computational tool, built upon MAGeCK, for CRISPR screening analysis.

Compared with MAGeCK, MAGeCK2 highlights the following additional functionalities:

• Paired sample analysis
• Processing and analyzing screens with UMIs
• Processing and analyzing paired-guide screens

See ROADMAP.md for the planned direction of the project.

MAGeCK2 is compatible with the lagacy MAGeCK. Everything is unchanged -- just need to switch the command from "mageck" to "mageck2".

Installation

MAGeCK2 requires Python ≥ 3.7 and a C++ compiler (used to build the bundled RRA component; g++ on Linux or clang++ on macOS, plus make). The Python dependencies (numpy, scipy, pandas, matplotlib, statsmodels) are installed automatically.

Install the latest release from PyPI:

pip install mageck2

To install the latest development version directly from GitHub:

pip install git+https://github.com/davidliwei/mageck2.git

or from a local clone:

git clone https://github.com/davidliwei/mageck2.git
cd mageck2
pip install .

For detailed instructions, see mageck2-doc.

Quick start

Run a statistical test from a count table:

mageck2 test -k count_table.txt -t treatment_samples -c control_samples -n output_prefix

Runnable example datasets are available in the mageck2-demo repository.

Documentation

For instructions on installation, usage and running examples, see mageck2-doc.

MAGeCK

The older version of MAGeCK can be accessed via sourceforge or bitbucket.

Contributing

Contributions are welcome. See CONTRIBUTING.md for how to get started, GOVERNANCE.md for how the project is run, and ROADMAP.md for where it is headed.

Questions

Questions? Bug? Recommendations? Here are a few ways:

• Join our Google group;
• Create an issue in the github repository. Issues from demo or documentations will need to be posted to mageck2-demo or mageck2-doc, respectively.

Version history

2026 — Version 0.2.0: Packaging modernization

• First release published to PyPI: pip install mageck2.
• Migrated packaging to pyproject.toml; MAGeCK2 is now pip-installable on Python 3.7+ (including 3.12 and 3.13).
• Added continuous integration and a smoke-test suite.
• Added project governance and contribution documentation.

See CHANGELOG.md for the full list of changes.

2020.12.01 Version 0.1

• Add paired-guide support in count command
• Add UMI support in count command
• The source code released.