AnanseScanpy package: 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 .
Install Jupyter Notebook
$ pip install jupyter
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://zenodo.org/record/7446267/files/rna_PBMC.h5ad -O scANANSE/rna_PBMC.h5ad
$ wget https://zenodo.org/record/7446267/files/atac_PBMC.h5ad -O scANANSE/atac_PBMC.h5ad
installing and running anansnake
Follow the instructions its respective github page, https://github.com/vanheeringen-lab/anansnake Next automatically use the generated files to run GRN analysis using your single cell cluster data:
snakemake --use-conda --conda-frontend mamba \
--configfile scANANSE/analysis/config.yaml \
--snakefile scANANSE/anansnake/Snakefile \
--resources mem_mb=48_000 --cores 12
Thanks to:
- Jos Smits and his Seurat equivalent of this package https://github.com/JGASmits/AnanseSeurat
- Siebren Frohlich and his anansnake implementation https://github.com/vanheeringen-lab/anansnake
1 maintainer
Metadata
1 maintainer
Release files for anansescanpy 1.0.0
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Total release size: 31.9 kB
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Release files / anansescanpy-1.0.0-py3-none-any.whl
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