BiocPyRanges-package: Conveniently access PyRanges functionalities from...

In hpages/BiocPyRanges: Conveniently access PyRanges functionalities from Bioconductor

Conveniently access PyRanges functionalities from Bioconductor

Description

PyRanges is a Python module for "efficient comparison of genomic intervals in Python".

BiocPyRanges is an R package that leverages the power of popular R/Python interface reticulate to make it convenient to access PyRanges functionalities from Bioconductor. In particular:

• It provides two utility functions for converting back and forth between GRanges and PyRanges objects. See ?conversions.

• For maximum convenience it also defines the pandas and pyranges global symbols (which are references to the corresponding Python modules) as well as utility functions to facilitate installation of these modules. See below.

Usage

## Wrappers for py_install() to facilitate installation of the Python
## modules required by BiocPyRanges:

install_pandas(method="auto", conda="auto")
install_pyranges(method="auto", conda="auto")

Arguments

method, conda

See ?py_install in the reticulate package.

References

PyRanges: https://github.com/biocore-NTNU/pyranges

PyRanges' documentation: https://biocore-NTNU.github.io/pyranges/

reticulate: https://cran.r-project.org/web/packages/reticulate/

See Also

• py_install in the reticulate package for installing Python modules into a virtual environment or Conda environment.

• GRanges objects defined in the GenomicRanges package.

• ?conversions for converting back and forth between GRanges and PyRanges objects.

hpages/BiocPyRanges documentation built on Aug. 21, 2023, 10:11 a.m.