## `AnanseScanpy` package: implementation of scANANSE for Scanpy objects in Python
[](https://anaconda.org/bioconda/anansescanpy)
[](https://badge.fury.io/py/anansescanpy)
[](http://bioconda.github.io/recipes/anansescanpy/README.html)
[](https://anaconda.org/bioconda/anansescanpy)
[](https://codeclimate.com/github/Arts-of-coding/AnanseScanpy/maintainability)
## 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
[](https://doi.org/10.5281/zenodo.7446267)
```
$ 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:
```{bash eval=FALSE}
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
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"description": "## `AnanseScanpy` package: implementation of scANANSE for Scanpy objects in Python\n[](https://anaconda.org/bioconda/anansescanpy)\n[](https://badge.fury.io/py/anansescanpy)\n[](http://bioconda.github.io/recipes/anansescanpy/README.html)\n[](https://anaconda.org/bioconda/anansescanpy)\n[](https://codeclimate.com/github/Arts-of-coding/AnanseScanpy/maintainability)\n\n\n## Installation\n\nThe most straightforward way to install the most recent version of AnanseScanpy is via conda using PyPI.\n\n### Install package through Conda\nIf you have not used Bioconda before, first set up the necessary channels (in this order!). \nYou only have to do this once.\n```\n$ conda config --add channels defaults\n$ conda config --add channels bioconda\n$ conda config --add channels conda-forge\n```\n\nThen install AnanseScanpy with:\n```\n$ conda install anansescanpy\n```\n\n### Install package through PyPI\n```\n$ pip install anansescanpy\n```\n\n### Install package through GitHub\n```\n$ git clone https://github.com/Arts-of-coding/AnanseScanpy.git\n$ cd AnanseScanpy\n$ conda env create -f requirements.yaml\n$ conda activate AnanseScanpy\n$ pip install -e .\n```\n\n### Install Jupyter Notebook\n```\n$ pip install jupyter\n```\n\n## Start using the package\n\n### Run the package either in the console\n```\n$ python3\n```\n\n### Or run the package in jupyter notebook\n```\n$ jupyter notebook\n```\n\n## For extended documentation see our ipynb vignette with PBMC sample data\n### Of which the sample data can be downloaded\n[](https://doi.org/10.5281/zenodo.7446267)\n```\n$ wget https://zenodo.org/record/7446267/files/rna_PBMC.h5ad -O scANANSE/rna_PBMC.h5ad\n$ wget https://zenodo.org/record/7446267/files/atac_PBMC.h5ad -O scANANSE/atac_PBMC.h5ad\n```\n\n### installing and running anansnake \n\nFollow the instructions its respective github page, https://github.com/vanheeringen-lab/anansnake\nNext automatically use the generated files to run GRN analysis using your single cell cluster data:\n\n\n```{bash eval=FALSE}\nsnakemake --use-conda --conda-frontend mamba \\\n--configfile scANANSE/analysis/config.yaml \\\n--snakefile scANANSE/anansnake/Snakefile \\\n--resources mem_mb=48_000 --cores 12\n```\n\n### Thanks to:\n\n* Jos Smits and his Seurat equivalent of this package https://github.com/JGASmits/AnanseSeurat\n* Siebren Frohlich and his anansnake implementation https://github.com/vanheeringen-lab/anansnake\n",
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