anansescanpy 0.1.9

implementation of scANANSE for scanpy objects in Python

AnanseScanpy: implementation of scANANSE for Scanpy objects in Python

Installation

The most straightforward way to install the most recent version of AnanseScanpy is via conda using PyPI.

Install package through Conda

If you have not used Bioconda before, first set up the necessary channels (in this order!). You only have to do this once.

$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge

Then install AnanseScanpy with:

$ conda install anansescanpy

Install package through PyPI

$ pip install anansescanpy

Install package through GitHub

git clone https://github.com/Arts-of-coding/AnanseScanpy.git
cd AnanseScanpy
conda env create -f requirements.yaml
conda activate AnanseScanpy
pip install -e .

Start using the package

Run the package either in the console

$ python3

Or run the package in jupyter notebook

$ jupyter notebook

For extended documentation see our ipynb vignette with PBMC sample data

Of which the sample data can be downloaded

$ wget https://mbdata.science.ru.nl/jsmits/scANANSE/rna_PBMC.h5ad -O scANANSE/rna_PBMC.h5ad
$ wget https://mbdata.science.ru.nl/jsmits/scANANSE/atac_PBMC.h5ad -O scANANSE/atac_PBMC.h5ad