sceps 0.1.0__tar.gz

sceps-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Genentech, Inc.
+
+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.

sceps-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sceps
+Version: 0.1.0
+Summary: Integrate GWAS and single-cell disease cell atlas data to identify disease-associated cell neighborhoods
+Author: Genentech, Inc.
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Genentech/sceps
+Project-URL: Documentation, https://github.com/Genentech/sceps/wiki
+Project-URL: Repository, https://github.com/Genentech/sceps
+Project-URL: Issues, https://github.com/Genentech/sceps/issues
+Keywords: single-cell,GWAS,genetics,transcriptomics,scRNA-seq
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<3,>=1.23
+Requires-Dist: pandas<3,>=1.5
+Requires-Dist: scipy<2,>=1.9
+Requires-Dist: anndata<1,>=0.10
+Requires-Dist: scanpy<2,>=1.10
+Requires-Dist: scikit-learn<2,>=1.1
+Requires-Dist: statsmodels<1,>=0.13
+Requires-Dist: tqdm>=4.60
+Requires-Dist: packaging>=20
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: seaborn>=0.12
+Provides-Extra: preprocess
+Requires-Dist: harmonypy>=0.0.9; extra == "preprocess"
+Dynamic: license-file
+
+# scEPS
+**scEPS** (single-cell Expression exPlainability Statistics)
+
+This repo contains the code of the method, **scEPS**, for integrating GWAS and single-cell disease cell atlas data to identify disease-associated cell neighborhoods. scEPS calculates a $d$ statistic at each cell neighborhood, representing the difference between the variance in disease explained by variations in the expression of each GWAS vs. each mean-expression matched control gene. An illustration of the scEPS method is shown below:
+
+![scEPS illustration](https://raw.githubusercontent.com/Genentech/sceps/master/img/scEPS_overview.png  "Overview of the scEPS method")
+
+# Reference
+
+The current draft of the manuscript is available [here](https://www.medrxiv.org/content/10.64898/2026.06.26.26356714v1). The code we used to create the figures in the manuscript is available [here](https://github.com/Genentech/sceps_manuscript). We also implemented [CNA*](https://github.com/Genentech/cna_star), a simple extension of [CNA](https://github.com/immunogenomics/cna), for estimating the variance in disease attributable to variations in cell abundance at each cell neighborhood.
+
+We also provide a web UI for visualizing the results in the scEPS manuscript [here](https://scepsresultexplorer.streamlit.app/).
+
+# Manual
+We provide a detailed manual of scEPS in the [Wiki page](https://github.com/Genentech/sceps/wiki).
+
+# Installation
+
+## Option 1: using pip
+
+The easiest way to install scEPS is from [PyPI](https://pypi.org/project/sceps/):
+```shell
+pip install sceps
+```
+
+This installs the `sceps` Python package along with the four command-line tools described under [Usage](#usage).
+
+## Option 2: using Anaconda or Miniforge
+scEPS may also be installed into a dedicated environment through [Anaconda](https://www.anaconda.com/download) or [Miniforge](https://github.com/conda-forge/miniforge). To do this, please first install Anaconda or Miniforge on your machine. You may then install scEPS using the following commands:
+``` shell
+git clone git@github.com:Genentech/sceps.git
+cd sceps
+conda env create -f sceps.yml
+conda activate sceps
+pip install .
+```
+
+The `sceps.yml` file installs the dependencies through conda; the final `pip install .` installs scEPS itself and its command-line tools. Use `pip install -e .` instead if you intend to modify the scEPS source.
+
+## Option 3: manually install required packages
+
+The user may also manually install the required packages to run scEPS. scEPS requires Python 3.9 or newer and the following packages:
+
+| Package | Minimum | Version pinned in `sceps.yml` |
+| --- | --- | --- |
+| [numpy](https://numpy.org/) | 1.23 | 1.26.2 |
+| [pandas](https://pandas.pydata.org/) | 1.5 | 1.5.3 |
+| [scipy](https://scipy.org/) | 1.9 | 1.13.1 |
+| [anndata](https://anndata.readthedocs.io/) | 0.10 | 0.10.7 |
+| [scanpy](https://scanpy.readthedocs.io/) | 1.10 | 1.10.3 |
+| [scikit-learn](https://scikit-learn.org/) | 1.1 | 1.3.2 |
+| [statsmodels](https://www.statsmodels.org/) | 0.13 | 0.14.5 |
+| [tqdm](https://tqdm.github.io/) | 4.60 | 4.67.1 |
+| [packaging](https://packaging.pypa.io/) | 20 | 25.0 |
+| [matplotlib](https://matplotlib.org/) | 3.6 | 3.9.4 |
+| [seaborn](https://seaborn.pydata.org/) | 0.12 | 0.13.2 |
+
+These can be installed with a single command:
+```shell
+conda install -c conda-forge python=3.9 numpy=1.26.2 pandas=1.5.3 scipy=1.13.1 \
+    anndata=0.10.7 scanpy=1.10.3 scikit-learn=1.3.2 statsmodels=0.14.5 \
+    tqdm=4.67.1 packaging=25.0 matplotlib-base=3.9.4 seaborn=0.13.2
+```
+
+The pinned versions are those used for the analyses in the manuscript, and `sceps.yml` reproduces that environment exactly. The minimums are the floors declared in `pyproject.toml`; scEPS has also been verified to reproduce identical output on numpy 2.x, pandas 2.x, anndata 0.12 and scanpy 1.11.
+
+The optional preprocessing helper script `misc/preprocess_scdata.py` additionally requires [harmonypy](https://github.com/slowkow/harmonypy) for batch integration. This is also available as an extra:
+```shell
+pip install "sceps[preprocess]"
+```
+
+Once the required packages to run scEPS are installed, the user may then install scEPS using:
+```shell
+git clone git@github.com:Genentech/sceps.git
+cd sceps
+pip install --no-deps .
+```
+
+# Usage
+
+Installing scEPS provides four command-line tools, corresponding to the four steps of the scEPS workflow:
+
+| Command | Purpose |
+| --- | --- |
+| `sceps` | Estimate scEPS statistics for individual cell neighborhoods |
+| `sceps-cluster-neighborhood` | Define approximately independent cell neighborhood blocks |
+| `sceps-aggregate` | Aggregate scEPS statistics across cell types and across all cells |
+| `sceps-corr` | Correlate scEPS statistics with gene expression |
+
+Pass `--help` to any of them for the full list of options, e.g. `sceps --help`. A detailed description of each step is available in the [Wiki page](https://github.com/Genentech/sceps/wiki).
+
+scEPS can also be driven from Python rather than the command line:
+```python
+from sceps.sceps_core import *
+```
+See [misc/run_sceps_from_python.py](https://github.com/Genentech/sceps/blob/master/misc/run_sceps_from_python.py) for a worked example.
+
+# Testing scEPS
+
+We provide examples script to test the scEPS workflow [here](https://github.com/Genentech/sceps/tree/master/test).
+
+# Contact
+
+Please create a GitHub issue if you experience any issue with running scEPS.

sceps-0.1.0/README.md

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+# scEPS
+**scEPS** (single-cell Expression exPlainability Statistics)
+
+This repo contains the code of the method, **scEPS**, for integrating GWAS and single-cell disease cell atlas data to identify disease-associated cell neighborhoods. scEPS calculates a $d$ statistic at each cell neighborhood, representing the difference between the variance in disease explained by variations in the expression of each GWAS vs. each mean-expression matched control gene. An illustration of the scEPS method is shown below:
+
+![scEPS illustration](https://raw.githubusercontent.com/Genentech/sceps/master/img/scEPS_overview.png  "Overview of the scEPS method")
+
+# Reference
+
+The current draft of the manuscript is available [here](https://www.medrxiv.org/content/10.64898/2026.06.26.26356714v1). The code we used to create the figures in the manuscript is available [here](https://github.com/Genentech/sceps_manuscript). We also implemented [CNA*](https://github.com/Genentech/cna_star), a simple extension of [CNA](https://github.com/immunogenomics/cna), for estimating the variance in disease attributable to variations in cell abundance at each cell neighborhood.
+
+We also provide a web UI for visualizing the results in the scEPS manuscript [here](https://scepsresultexplorer.streamlit.app/).
+
+# Manual
+We provide a detailed manual of scEPS in the [Wiki page](https://github.com/Genentech/sceps/wiki).
+
+# Installation
+
+## Option 1: using pip
+
+The easiest way to install scEPS is from [PyPI](https://pypi.org/project/sceps/):
+```shell
+pip install sceps
+```
+
+This installs the `sceps` Python package along with the four command-line tools described under [Usage](#usage).
+
+## Option 2: using Anaconda or Miniforge
+scEPS may also be installed into a dedicated environment through [Anaconda](https://www.anaconda.com/download) or [Miniforge](https://github.com/conda-forge/miniforge). To do this, please first install Anaconda or Miniforge on your machine. You may then install scEPS using the following commands:
+``` shell
+git clone git@github.com:Genentech/sceps.git
+cd sceps
+conda env create -f sceps.yml
+conda activate sceps
+pip install .
+```
+
+The `sceps.yml` file installs the dependencies through conda; the final `pip install .` installs scEPS itself and its command-line tools. Use `pip install -e .` instead if you intend to modify the scEPS source.
+
+## Option 3: manually install required packages
+
+The user may also manually install the required packages to run scEPS. scEPS requires Python 3.9 or newer and the following packages:
+
+| Package | Minimum | Version pinned in `sceps.yml` |
+| --- | --- | --- |
+| [numpy](https://numpy.org/) | 1.23 | 1.26.2 |
+| [pandas](https://pandas.pydata.org/) | 1.5 | 1.5.3 |
+| [scipy](https://scipy.org/) | 1.9 | 1.13.1 |
+| [anndata](https://anndata.readthedocs.io/) | 0.10 | 0.10.7 |
+| [scanpy](https://scanpy.readthedocs.io/) | 1.10 | 1.10.3 |
+| [scikit-learn](https://scikit-learn.org/) | 1.1 | 1.3.2 |
+| [statsmodels](https://www.statsmodels.org/) | 0.13 | 0.14.5 |
+| [tqdm](https://tqdm.github.io/) | 4.60 | 4.67.1 |
+| [packaging](https://packaging.pypa.io/) | 20 | 25.0 |
+| [matplotlib](https://matplotlib.org/) | 3.6 | 3.9.4 |
+| [seaborn](https://seaborn.pydata.org/) | 0.12 | 0.13.2 |
+
+These can be installed with a single command:
+```shell
+conda install -c conda-forge python=3.9 numpy=1.26.2 pandas=1.5.3 scipy=1.13.1 \
+    anndata=0.10.7 scanpy=1.10.3 scikit-learn=1.3.2 statsmodels=0.14.5 \
+    tqdm=4.67.1 packaging=25.0 matplotlib-base=3.9.4 seaborn=0.13.2
+```
+
+The pinned versions are those used for the analyses in the manuscript, and `sceps.yml` reproduces that environment exactly. The minimums are the floors declared in `pyproject.toml`; scEPS has also been verified to reproduce identical output on numpy 2.x, pandas 2.x, anndata 0.12 and scanpy 1.11.
+
+The optional preprocessing helper script `misc/preprocess_scdata.py` additionally requires [harmonypy](https://github.com/slowkow/harmonypy) for batch integration. This is also available as an extra:
+```shell
+pip install "sceps[preprocess]"
+```
+
+Once the required packages to run scEPS are installed, the user may then install scEPS using:
+```shell
+git clone git@github.com:Genentech/sceps.git
+cd sceps
+pip install --no-deps .
+```
+
+# Usage
+
+Installing scEPS provides four command-line tools, corresponding to the four steps of the scEPS workflow:
+
+| Command | Purpose |
+| --- | --- |
+| `sceps` | Estimate scEPS statistics for individual cell neighborhoods |
+| `sceps-cluster-neighborhood` | Define approximately independent cell neighborhood blocks |
+| `sceps-aggregate` | Aggregate scEPS statistics across cell types and across all cells |
+| `sceps-corr` | Correlate scEPS statistics with gene expression |
+
+Pass `--help` to any of them for the full list of options, e.g. `sceps --help`. A detailed description of each step is available in the [Wiki page](https://github.com/Genentech/sceps/wiki).
+
+scEPS can also be driven from Python rather than the command line:
+```python
+from sceps.sceps_core import *
+```
+See [misc/run_sceps_from_python.py](https://github.com/Genentech/sceps/blob/master/misc/run_sceps_from_python.py) for a worked example.
+
+# Testing scEPS
+
+We provide examples script to test the scEPS workflow [here](https://github.com/Genentech/sceps/tree/master/test).
+
+# Contact
+
+Please create a GitHub issue if you experience any issue with running scEPS.

sceps-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sceps"
+version = "0.1.0"
+description = "Integrate GWAS and single-cell disease cell atlas data to identify disease-associated cell neighborhoods"
+readme = "README.md"
+requires-python = ">=3.9"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{ name = "Genentech, Inc." }]
+keywords = ["single-cell", "GWAS", "genetics", "transcriptomics", "scRNA-seq"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+# Lower bounds are the versions scEPS has been tested against; majors are capped
+# because this is an analysis tool rather than a library, so a breaking upstream
+# release should fail at resolution time and not halfway through a long run.
+dependencies = [
+    "numpy>=1.23,<3",
+    "pandas>=1.5,<3",
+    "scipy>=1.9,<2",
+    "anndata>=0.10,<1",
+    "scanpy>=1.10,<2",
+    "scikit-learn>=1.1,<2",
+    "statsmodels>=0.13,<1",
+    "tqdm>=4.60",
+    "packaging>=20",
+    # Imported by sceps/estimation.py. scanpy depends on both as well, but scEPS
+    # imports them directly, so they are declared directly.
+    "matplotlib>=3.6",
+    "seaborn>=0.12",
+]
+
+[project.optional-dependencies]
+# Only needed by the misc/preprocess_scdata.py helper (sce.pp.harmony_integrate).
+preprocess = ["harmonypy>=0.0.9"]
+
+[project.urls]
+Homepage = "https://github.com/Genentech/sceps"
+Documentation = "https://github.com/Genentech/sceps/wiki"
+Repository = "https://github.com/Genentech/sceps"
+Issues = "https://github.com/Genentech/sceps/issues"
+
+[project.scripts]
+sceps = "sceps.cli.run:main"
+sceps-cluster-neighborhood = "sceps.cli.cluster_neighborhood:main"
+sceps-aggregate = "sceps.cli.aggregate:main"
+sceps-corr = "sceps.cli.corr:main"
+
+[tool.setuptools.packages.find]
+# Ship only the importable package; test/, misc/ and img/ stay out of the wheel.
+include = ["sceps*"]

sceps-0.1.0/sceps/__init__.py

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+"""scEPS (single-cell Expression exPlainability Statistics).
+
+Integrates GWAS and single-cell disease cell atlas data to identify
+disease-associated cell neighborhoods.
+
+The Python API lives in :mod:`sceps.sceps_core`::
+
+    from sceps.sceps_core import *
+
+Nothing heavyweight is imported here on purpose: the console scripts in
+``sceps.cli`` import this package first, and pulling scanpy in at this point
+would slow down ``--help`` for every command.
+"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("sceps")
+except PackageNotFoundError:  # running from a source tree without an install
+    __version__ = "0.0.0.dev0"
+
+__all__ = ["__version__"]

sceps-0.1.0/sceps/cli/__init__.py

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+"""Command-line entry points for scEPS.
+
+Each module here exposes a ``main()`` that is wired to a console script in
+``pyproject.toml``:
+
+==============================  ==============================
+command                         module
+==============================  ==============================
+``sceps``                       :mod:`sceps.cli.run`
+``sceps-cluster-neighborhood``  :mod:`sceps.cli.cluster_neighborhood`
+``sceps-aggregate``             :mod:`sceps.cli.aggregate`
+``sceps-corr``                  :mod:`sceps.cli.corr`
+==============================  ==============================
+"""