An iFISH probe design pipeline, with web interface included.
Project description
iFISH-Probe-Design
iFISH-Probe-Design (ifpd
) is a Python3.7+ 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.
Requirements
iFISH-Probe-Designer is fully implemented in Python3.7+, thus you need Python3 to run it. Check out here how to install Python3.7+ on your machine if you don't have it yet.
ifpd
has been tested with Python 3.7, 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.
Installation
We recommend installing ifpd
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 ifpd
by running: pipx install ifpd
. If you see the stars (✨ 🌟 ✨), then the installation went well!
Usage
All iFISH-Probe-Design commands are accessible via the ifpd
keyword on the terminal. For each command, you can access its help page by using the -h
option. More details on how to run ifpd
are available in the online documentation.
Contributing
We welcome any contributions to ifpd
. 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.
Reference
- Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., ... & Bienko, M. (2019). iFISH is a publicly available resource enabling versatile DNA FISH to study genome architecture. Nature communications, 10(1), 1-15. (link)
License
MIT License - Copyright (c) 2016-21 Gabriele Girelli
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