looptrace is a software suite for chromatin tracing image and data analysis as described in https://doi.org/10.1101/2021.04.12.439407
We expect that in most cases looptrace will be used as a processing pipeline, with perhaps some post-hoc analysis of the resulting, processed data.
For that, we have a Docker image and documentation on how to run the pipeline.
To use looptrace in more of a package / library fashion, you may work with various components of the Python package and/or the Scala library.
In either case, we recommend to install Nix and then use this project's Nix shell with whatever --arg <argname> true values you need to pull in the dependency group(s) needed for your use case.
Written by Kai Sandvold Beckwith ([email protected]), Ellenberg group, CBB, EMBL Heidelberg.
Extended and maintained by Vincent Reuter, Gerlich group, Institute for Molecular Biotechnology (IMBA) in Vienna, Austria. See https://www.oeaw.ac.at/imba/research/daniel-gerlich/
Please cite this paper: https://www.biorxiv.org/content/10.1101/2021.04.12.439407