oddSNP 0.1.0__tar.gz

oddsnp-0.1.0/LICENSE

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oddsnp-0.1.0/NOTICE

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+Project: oddSNP
+
+This software was developed as part of academic research.
+
+Copyright 2025-266 Nemoto-lab, The University of Osaka
+
+Contributors:
+
+* Rodolfo Allendes
+* Takahiro Nemoto
+
+Affiliation:
+
+* Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), The University of Osaka.
+
+If you use this software in academic work, please consider citing the associated publication.

oddsnp-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: oddSNP
+Version: 0.1.0
+Summary: A CLI tool for Optimizing demultiplexing pooled experiments based on Single-Nuclotide Polymorphism
+Author-email: Rodolfo Allendes <rodolfo.allendes.prime@osaka-u.ac.jp>, Takahiro Nemoto <nemoto.takahiro.prime@osaka-u.ac.jp>
+Project-URL: Homepage, https://github.com/nemoto-lab/oddSNP
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: click
+Requires-Dist: pandas
+Requires-Dist: pysam
+Requires-Dist: plotly
+Requires-Dist: nbformat
+Requires-Dist: kaleido
+Requires-Dist: tqdm
+Requires-Dist: more_itertools
+Requires-Dist: joblib
+Requires-Dist: requests
+Requires-Dist: ipykernel
+Requires-Dist: threadpoolctl
+Requires-Dist: vireoSNP
+Dynamic: license-file
+
+<p align="center">
+  <img src="docs/source/_static/banner.png" width=300px>
+</p>
+
+Donor multiplexing is a powerful strategy to increase scale, lower the costs, and reduce batch effects in single-cell RNA sequencing (scRNAseq), but clear guidelines for experimental design are lacking, forcing researchers to risk costly demultiplexing failures. To address this, we introduce SNP-Information Content (SNP-IC) and cell-paird SNP-Information Content (cpSNP-IC), quantitative metrics that can be computed from simple, unpooled pilot data and that accurately predict the success of demultiplexing. *oddSNP* is an open-source framework for computing these metrics, enabling in-silico titration of sequencing depth and donor complexity to optimize experimental design before committing to large-scale studies. 
+
+Details on these metrics and the implementation of the tool are available in the manuscript entitled: *OddSNP: a predictive framework for optimizing multiplexed single-cell RNA-seq* ([https://doi.org/10.64898/2025.12.08.692882](https://doi.org/10.64898/2025.12.08.692882)).
+
+*oddSNP* is developed at the Nemoto-lab, The University of Osaka.
+
+The full documentation of *oddSNP* is available at:
+https://nemoto-lab.github.io/oddSNP/
+
+
+## Installation
+
+The recommended way to install *oddSNP* is by using a virtual environments manager such as [Conda](https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html) (or [venv](https://docs.python.org/3/library/venv.html)). 
+
+### Using Bioconda:
+
+We create a new conda environment and directly install *oddSNP* from its bioconda source.
+
+```bash
+:~$ conda create --name oddsnp
+:~$ conda activate oddsnp
+(oddsnp):~$ conda install -c bioconda oddsnp
+```
+
+### Using PyPI:
+
+Still, we recommend to install *oddSNP* inside a virtual environment. In this case, we need to make sure to also install `pip` to the created environment to avoid interfering with system libraries.
+
+```bash
+:~$ conda create --name oddsnp
+:~$ conda activate oddsnp
+(oddsnp):~$ conda install pip
+(oddsnp):~$ pip install oddsnp
+```
+
+### From source:
+
+Details on how to install *oddSNP* from source are given in the [Tutorial notebook](notebooks/tutorial.ipynb).
+
+### After installation
+
+An installation of [cellsnp-lite](https://cellsnp-lite.readthedocs.io/en/latest/index.html) is required to perform pileup calculations within oddSNP. To install it, use the following command inside your activated conda environment:
+
+```bash
+(oddsnp):~$ conda install -c bioconda cellsnp-lite 
+```
+
+**NOTE** Other installation methods for `cellsnp-lite` are described in their [original website](https://cellsnp-lite.readthedocs.io/en/latest/index.html).
+
+
+
+To check the installation finished properly, we can try and run *oddSNP* from the command line without any sub-commands. The output should be as follows:
+
+```bash
+(oddsnp):~$ oddSNP 
+Usage: oddSNP [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  --help  Show this message and exit.
+
+Commands:
+  cpsnpic
+  downsample
+  genotype
+  snpic
+  utils
+```
+
+## Using oddSNP
+
+For details on how to use *oddSNP* please refer to the accompanying tutorial notebook: [tutorial.ipynb](notebooks/tutorial.ipynb)
+
+## 📄 How to Cite
+
+If you use this repository in your research, please cite our bioRxiv preprint:
+
+> **OddSNP: a predictive framework for optimizing multiplexed single-cell RNA sequencing**  
+> Allendes Osorio, R.S., Nishimura, T., Shigihara, Y., Kimura, M., Takebe, T. and Nemoto, T. (2025)  
+> https://www.biorxiv.org/content/10.64898/2025.12.08.692882v1
+
+### BibTeX
+
+```bibtex
+@article{osorio2025oddsnp,
+  title   = {OddSNP: a predictive framework for optimizing multiplexed single-cell RNA sequencing},
+  author  = {Allendes Osorio, R.S. and Nishimura, T. and Shigihara, Y. and Kimura, M. and Takebe, T. and Nemoto, T.},
+  journal = {bioRxiv},
+  year    = {2025},
+  doi     = {10.64898/2025.12.08.692882},
+  url     = {https://www.biorxiv.org/content/10.64898/2025.12.08.692882v1},
+  note    = {Preprint}
+}
+```

oddsnp-0.1.0/README.md

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+<p align="center">
+  <img src="docs/source/_static/banner.png" width=300px>
+</p>
+
+Donor multiplexing is a powerful strategy to increase scale, lower the costs, and reduce batch effects in single-cell RNA sequencing (scRNAseq), but clear guidelines for experimental design are lacking, forcing researchers to risk costly demultiplexing failures. To address this, we introduce SNP-Information Content (SNP-IC) and cell-paird SNP-Information Content (cpSNP-IC), quantitative metrics that can be computed from simple, unpooled pilot data and that accurately predict the success of demultiplexing. *oddSNP* is an open-source framework for computing these metrics, enabling in-silico titration of sequencing depth and donor complexity to optimize experimental design before committing to large-scale studies. 
+
+Details on these metrics and the implementation of the tool are available in the manuscript entitled: *OddSNP: a predictive framework for optimizing multiplexed single-cell RNA-seq* ([https://doi.org/10.64898/2025.12.08.692882](https://doi.org/10.64898/2025.12.08.692882)).
+
+*oddSNP* is developed at the Nemoto-lab, The University of Osaka.
+
+The full documentation of *oddSNP* is available at:
+https://nemoto-lab.github.io/oddSNP/
+
+
+## Installation
+
+The recommended way to install *oddSNP* is by using a virtual environments manager such as [Conda](https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html) (or [venv](https://docs.python.org/3/library/venv.html)). 
+
+### Using Bioconda:
+
+We create a new conda environment and directly install *oddSNP* from its bioconda source.
+
+```bash
+:~$ conda create --name oddsnp
+:~$ conda activate oddsnp
+(oddsnp):~$ conda install -c bioconda oddsnp
+```
+
+### Using PyPI:
+
+Still, we recommend to install *oddSNP* inside a virtual environment. In this case, we need to make sure to also install `pip` to the created environment to avoid interfering with system libraries.
+
+```bash
+:~$ conda create --name oddsnp
+:~$ conda activate oddsnp
+(oddsnp):~$ conda install pip
+(oddsnp):~$ pip install oddsnp
+```
+
+### From source:
+
+Details on how to install *oddSNP* from source are given in the [Tutorial notebook](notebooks/tutorial.ipynb).
+
+### After installation
+
+An installation of [cellsnp-lite](https://cellsnp-lite.readthedocs.io/en/latest/index.html) is required to perform pileup calculations within oddSNP. To install it, use the following command inside your activated conda environment:
+
+```bash
+(oddsnp):~$ conda install -c bioconda cellsnp-lite 
+```
+
+**NOTE** Other installation methods for `cellsnp-lite` are described in their [original website](https://cellsnp-lite.readthedocs.io/en/latest/index.html).
+
+
+
+To check the installation finished properly, we can try and run *oddSNP* from the command line without any sub-commands. The output should be as follows:
+
+```bash
+(oddsnp):~$ oddSNP 
+Usage: oddSNP [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  --help  Show this message and exit.
+
+Commands:
+  cpsnpic
+  downsample
+  genotype
+  snpic
+  utils
+```
+
+## Using oddSNP
+
+For details on how to use *oddSNP* please refer to the accompanying tutorial notebook: [tutorial.ipynb](notebooks/tutorial.ipynb)
+
+## 📄 How to Cite
+
+If you use this repository in your research, please cite our bioRxiv preprint:
+
+> **OddSNP: a predictive framework for optimizing multiplexed single-cell RNA sequencing**  
+> Allendes Osorio, R.S., Nishimura, T., Shigihara, Y., Kimura, M., Takebe, T. and Nemoto, T. (2025)  
+> https://www.biorxiv.org/content/10.64898/2025.12.08.692882v1
+
+### BibTeX
+
+```bibtex
+@article{osorio2025oddsnp,
+  title   = {OddSNP: a predictive framework for optimizing multiplexed single-cell RNA sequencing},
+  author  = {Allendes Osorio, R.S. and Nishimura, T. and Shigihara, Y. and Kimura, M. and Takebe, T. and Nemoto, T.},
+  journal = {bioRxiv},
+  year    = {2025},
+  doi     = {10.64898/2025.12.08.692882},
+  url     = {https://www.biorxiv.org/content/10.64898/2025.12.08.692882v1},
+  note    = {Preprint}
+}
+```

oddsnp-0.1.0/pyproject.toml

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+# pyproject.toml for the oddSNP project
+# See: https://peps.python.org/pep-0621/ for project table keys
+
+[build-system]
+requires = ["setuptools"]
+
+[project]
+# Basic project metadata 
+name = "oddSNP"
+version = "0.1.0"
+
+# Contact information
+authors = [
+  { name="Rodolfo Allendes", email="rodolfo.allendes.prime@osaka-u.ac.jp" },
+  { name="Takahiro Nemoto", email="nemoto.takahiro.prime@osaka-u.ac.jp" }
+]
+
+description = "A CLI tool for Optimizing demultiplexing pooled experiments based on Single-Nuclotide Polymorphism"
+readme = "README.md"
+
+# Minimum version of python supported 
+requires-python = ">=3.12"
+
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+
+# Runtime dependencies
+dependencies = [
+  "click",
+  "pandas",
+  "pysam",
+  "plotly",
+  "nbformat",
+  "kaleido",
+  "tqdm",
+  "more_itertools",
+  "joblib",
+  "requests",
+  "ipykernel",
+  "threadpoolctl",
+  "vireoSNP",
+]
+# cellsnp-lite needs to be installed with conda
+
+[project.urls]
+Homepage = "https://github.com/nemoto-lab/oddSNP"
+#Issues = "https://github.com/pypa/sampleproject/issues"
+
+# This is required for the project to be recognized as a command-line tool 
+# and provides an access point to it 
+[project.scripts]
+oddSNP = "oddSNP.__main__:oddSNP"
+

oddsnp-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

oddsnp-0.1.0/src/oddSNP/__init__.py

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+"""oddSNP is an open-source framework for the calculation of SNP-Information 
+Content (SNP-IC), a quantitative metric computable from simple unpooled pilot 
+data that accurately predicts the success of genotype-based demultiplexing; 
+and its equivalent for genotype-free approaches, cell-paired SNP-Information 
+Content (cpSNP-IC)."""
+
+__version__ = '0.1.0'
+__author__ = 'Rodolfo Allendes'
+__email__ = 'rodolfo.allendes.prime@osaka-u.ac.jp'
+
+# make oddSNP available if someone imports
+from .__main__ import oddSNP as main
+
+__all__ = ['main']

oddsnp-0.1.0/src/oddSNP/__main__.py

@@ -0,0 +1,33 @@
+# Copyright (C) 2025 Nemoto-lab, Osaka University
+# email: rodolfo.allendes.prime@osaka-u.ac.jp
+# email: nemoto.takahiro.prime@osaka-u.ac.jp
+#
+# This program is free software; you can redistribute it and/or modify it under 
+# the terms of the GNU General Public License as published by the Free Software 
+# Foundation; either version 2 of the License, or (at your option) any later 
+# version.
+# This program is distributed in the hope that it will be useful, but WITHOUT 
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License along with 
+# this program; if not, write to the Free Software Foundation, Inc., 59 Temple 
+# Place, Suite 330, Boston, MA 02111-1307 USA
+import click
+
+from . import utils
+from . import downsampling
+from . import genotype
+from . import snpic
+from . import cpsnpic
+
+@click.group()
+@click.version_option(version='0.1.0', prog_name='oddSNP')
+def oddSNP():
+  pass
+
+oddSNP.add_command(utils.utils)
+oddSNP.add_command(downsampling.downsample)
+oddSNP.add_command(genotype.genotype)
+oddSNP.add_command(snpic.snpic)
+oddSNP.add_command(cpsnpic.cpsnpic)