RepTile

Inference of single-locus DNA replication states from genome-wide multiplexed DNA FISH.

Installation

We recommend using Python 3.11:

conda create -n img python=3.11 -y
conda activate img

First, make sure to install the alabtools library (https://github.com/alberlab/alabtools).

Then, install with conda-forge the following dependencies:

conda install -c conda-forge \
    trimesh \
    scikit-learn \
    pydantic \
    imbalanced-learn \
    xgboost \
    libspatialindex \
    rtree \
    statsmodels \
    mrcfile \
    alphashape \
    -y

Finally, install RepTile:

pip install git+https://github.com/alberlab/RepTile.git

Usage

from reptile.cte import ChromatinTracingExperiment