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".
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.
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.
For instructions on installation, usage and running examples, see mageck2-doc.
The older version of MAGeCK can be accessed via sourceforge or bitbucket.
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? 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.
- 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.
- Add paired-guide support in count command
- Add UMI support in count command
- The source code released.