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BiocPy

Installs all BiocPy packages. The package itself does not provide any functionality on its own. It provides an

  • easier way to install all core packages
  • an interface to access the base data representations or classes

Install

Package is published to PyPI

pip install biocpy

Usage

To import any of the data classes,

from biocpy.genomicranges import GenomicRanges
from biocpy.summarizedexperiment import SummarizedExperiment
from biocpy.singlecellexperiment import SingleCellExperiment 
from biocpy.multiassayexperiment import MultiAssayExperiment

gr = GenomicRange(...)
se = SummarizedExperiment(...)
sce = SingleCellExperiment(...)
mae = MultiAssayExperiment(...)

For more use cases, checkout the documentation.

Note

This project has been set up using PyScaffold 4.1.1. For details and usage information on PyScaffold see https://pyscaffold.org/.

biocpy's Projects

assorthead icon assorthead

Assorted C++ headers, vendored into a Python package.

biocpy icon biocpy

Interface to all BiocPy packages

biocutils icon biocutils

Miscellaneous utilities for BiocPy, mostly to mimic base functionality in R.

cellarr icon cellarr

Store collections of experimental data based on TileDB

celldex icon celldex

Collection of reference cell type datasets

cpptypes icon cpptypes

Automatically generate wrappers for ctypes with C++

genomicranges icon genomicranges

Container class to represent genomic locations and support genomic analysis

scranpy icon scranpy

Single-cell data analysis, from C++ to Python

scrnaseq icon scrnaseq

Collection of public single-cell RNA-seq datasets

singler icon singler

Python bindings to the SingleR algorithm

tutorial icon tutorial

tutorial for all bioconductor representations in Python

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