| Name | singlecell-cookbook JSON |
| Version |
0.3.1
JSON |
| download |
| home_page | None |
| Summary | A collection of tools for analyzing single-cell genomics data. |
| upload_time | 2024-12-19 00:53:42 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | <3.13,>=3.11 |
| license | MIT License Copyright (c) 2024 Argenis Arriojas Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
rna-seq
analysis
bioinformatics
genomics
single-cell
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# singlecell-cookbook
[](https://github.com/argearriojas/singlecell-cookbook/actions/workflows/tests.yml)
A collection of tools for analyzing single-cell genomics data.
## Installation
You can install the package using pip:
```bash
pip install singlecell-cookbook
```
For development installation:
```bash
git clone https://github.com/argearriojas/singlecell-cookbook.git
cd singlecell-cookbook
pip install -e ".[dev]"
```
### R Dependencies
Some features (like pseudobulk analysis) require R and specific R packages. To use these features:
1. Install the required R packages in R:
```R
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("edgeR", "MAST"))
```
2. Install the R dependencies in Python:
```bash
pip install "singlecell-cookbook[r]"
```
## Documentation
Documentation is available at [Read the Docs](https://singlecell-cookbook.readthedocs.io/).
## Development
To set up the development environment:
1. Clone the repository
2. Install development dependencies: `pip install -e ".[dev]"`
3. Install pre-commit hooks: `pre-commit install`
## License
TBD. We need to assess the license according to the imported packages.
## Author
Argenis Arriojas ([arriojasmaldonado001@umb.edu](mailto:arriojasmaldonado001@umb.edu))
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"description": "# singlecell-cookbook\n\n[](https://github.com/argearriojas/singlecell-cookbook/actions/workflows/tests.yml)\n\nA collection of tools for analyzing single-cell genomics data.\n\n## Installation\n\nYou can install the package using pip:\n\n```bash\npip install singlecell-cookbook\n```\n\nFor development installation:\n\n```bash\ngit clone https://github.com/argearriojas/singlecell-cookbook.git\ncd singlecell-cookbook\npip install -e \".[dev]\"\n```\n\n### R Dependencies\n\nSome features (like pseudobulk analysis) require R and specific R packages. To use these features:\n\n1. Install the required R packages in R:\n\n```R\nif (!require(\"BiocManager\", quietly = TRUE))\n install.packages(\"BiocManager\")\n\nBiocManager::install(c(\"edgeR\", \"MAST\"))\n```\n\n2. Install the R dependencies in Python:\n\n```bash\npip install \"singlecell-cookbook[r]\"\n```\n\n## Documentation\n\nDocumentation is available at [Read the Docs](https://singlecell-cookbook.readthedocs.io/).\n\n## Development\n\nTo set up the development environment:\n\n1. Clone the repository\n2. Install development dependencies: `pip install -e \".[dev]\"`\n3. Install pre-commit hooks: `pre-commit install`\n\n## License\n\nTBD. We need to assess the license according to the imported packages.\n\n## Author\n\nArgenis Arriojas ([arriojasmaldonado001@umb.edu](mailto:arriojasmaldonado001@umb.edu))\n",
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