Welcome to handygenome’s documentation!

Indices and tables

• Index

• Module Index

• Search Page

Install

You can install handygenome by running the commands below,

conda create -n handygenome python>=3.10 bioconda::pysam conda-forge::rpy2 bioconda::bioconductor-dnacopy conda-forge::gcc
conda activate handygenome
pip install handygenome

which 1) makes a conda environment to install rpy2 using R with DNAcopy package, 2) then installs remaining python dependencies with pip.

Including all dependencies in a single conda package could not be achived due to package conflicts.

Python Dependencies

• numpy

• pandas

• matplotlib

• biopython >= 1.80

• pysam

• pyranges

• scipy

• scikit-learn

• PyYAML

• jupyterlab