biocpy / singlecellexperiment

Container class for single-cell experiments

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/.

singlecellexperiment's Issues

concat SingleCellExperiments

provide functionality to concatenate SingleCellExperiments

`toAnnData` should transform features to a `Pandas DataFrame` if its a `GenomicRanges` object

export sce from python

hello, the package is very cool to convert annadata into sce format. May i ask a question, please? How do i export the sce object to be able to load into R? Thanks a lot.

Why does SCE default to `None` for the alternative experiments?

import singlecellexperiment
import numpy
sce = singlecellexperiment.SingleCellExperiment({ "counts": numpy.random.rand(100, 10) })
print(sce.alternative_experiments)
## None

This should just be initialized as a dict and save us all the trouble of having to set it on first use. The same applies to everything else in the BiocPy suite; things should be initialized and ready for use.

`uns` may not be a dictionary when reading H5AD files

export sample mapping to uns

export to MuData

SingleCellExperiment should extend RangedSummarizedExperiment

SingleCellExperiment/src/singlecellexperiment/SingleCellExperiment.py

Line 21 in b808f7c

class SingleCellExperiment(SummarizedExperiment):

@jkanche according to bioconductor: https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html the SingleCellExperiment class should extend the RangedSummarizedExperiment class...

validate alternative experiments; must contain the same number of cells

Export BaseSE class

As it is used to type the experiment field a developer needs easy access to it when they want to use type hints.