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An iFISH probe design pipeline (II)

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iFISH Probe Design (II)

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ifpd2 is a Python3.8+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It is based on our previous ifpd package, but works with a different and more detailed database format, allowing for more precise control on the probe design process. Read the online documentation for more details.


ifpd2 is fully implemented in Python3.8+, thus you need the corresponding Python version to run it. Check out here how to install Python+ on your machine if you don't have it yet.

ifpd2 has been tested with Python 3.8 and 3.9. We recommend installing it using pipx (see below) to avoid dependency conflicts with other packages. The packages it depends on are listed in our dependency graph. We use poetry to handle our dependencies.


We recommend installing ifpd2 using pipx. Check how to install pipx here if you don't have it yet!

Once you have pipx ready on your system, install the latest stable release of ifpd2 by running: pipx install ifpd2. If you see the stars (✨ 🌟 ✨), then the installation went well!


All ifpd2 commands are accessible via the ifpd2 keyword on the terminal. For each command, you can access its help page by using the -h option. More details on how to run ifpd2 are available in the online documentation.


We welcome any contributions to ifpd2. In short, we use black to standardize code format. Any code change also needs to pass mypy checks. For more details, please refer to our contribution guidelines if this is your first time contributing! Also, check out our code of conduct.


MIT License - Copyright (c) 2021 Gabriele Girelli

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