A tool to process and analyze iTP-Seq datasets
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Project description
itpseq: A Python module and command-line tool for the analysis of iTP-Seq data.
The latest documentation is available at itpseq.readthedocs.io.
Dependencies
itpseq runs on Python 3.9+ on Linux, MacOS, and Windows.
Installation requires regex, numpy, pandas, matplotlib, seaborn, pydeseq2, logomaker, Jinja2, weasyprint, ipython, click, and ipywidgets. The dependencies are installed automatically when installing from pip.
Installation
The latest stable release (and required dependencies) can be installed from PyPI:
pip install itpseq
To update the package to the latest version, run:
pip install -U itpseq
After installation, if Python and pip are configured correctly, the "itpseq" command should be available in the terminal. If not, one should ensure the location of the executable is in the PATH.
Citing
Known issues
On MacOS and Windows, the "weasyprint" library that is used to produce the PDF version of the report seems to have an issue and exporting a PDF report is currently not possible. It is nevertheless possible to produce an HTML report by running:
itpseq report -o report.html data_directory
in place of:
itpseq report data_directory
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