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An iFISH probe design pipeline, with web interface included.

Project description



iFISH-Probe-Design (ifpd) is a Python3 package containing tools for selection of complementary oligonucleotides to build iFISH probes. It also includes a web interface, which simplifies the procedure by removing any requirement for programming skills. Read the online documentation for more details.


If you have Python3.6+ and pip3 installed on your computer, you can simply run sudo -H pip3 install ifpd on a terminal. That's it! As easy as it gets.

You can also install from github (any point in history, although we suggest to stick with release tags) as follows:

git clone
cd iFISH-probe-design
sudo -H pip3 install .

For a nice guide on installing packages served through PyPI, check out this tutorial.


iFISH-Probe-Designer is fully implemented in Python3, thus you need Python3 to run it. Check out here how to install Python3 on your machine if you don't have it yet.

If you installed this package using pip3 (as explained above), then all required libraries were also automatically installed. Nonetheless, here is a list (with version) of the required libraries:

  • bottle>=0.12.13 and paste>=2.0.3: to run the web server interface.
  • ggc>=0.0.3: for functionalities common to all my packages.
  • matplotlib>=3.0.0: to plot.
  • numpy>=1.14.2, pandas>=0.22.0, and scipy>=1.0.0: for data manipulation.


More details on how to run iFISH-Probe-Design are available in the online documentation.


We welcome any contributions to iFISH-Probe-Design. Please, refer to the contribution guidelines if this is your first time contributing! Also, check out our code of conduct.


MIT License
Copyright (c) 2016-2019 Gabriele Girelli

Project details

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