Skip to main content

An iFISH probe design pipeline, with web interface included.

Project description

iFISH-Probe-Design

DOI
PyPI - Python Version PyPI - Format PyPI - Status

PyPi | docs

iFISH-Probe-Design (ifpd) is a Python3.6.1+ 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 Python3.6.1+, thus you need Python3 to run it. Check out here how to install Python3.6.1+ on your machine if you don't have it yet.

ifpd has been tested with Python 3.6.1, 3.7, and 3.8. 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 publically 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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for ifpd, version 2.0.5
Filename, size File type Python version Upload date Hashes
Filename, size ifpd-2.0.5-py3-none-any.whl (7.2 MB) File type Wheel Python version py3 Upload date Hashes View
Filename, size ifpd-2.0.5.tar.gz (7.2 MB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page