densr 0.1.0__tar.gz

densr-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: densr
+Version: 0.1.0
+Summary: Density-aware spatial randomization and object-based colocalization analysis for 3D RNA spot data.
+Author: Sudharsan Kannan
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=1.5
+Requires-Dist: scipy>=1.9
+Requires-Dist: trimesh>=3.20
+Requires-Dist: rtree>=1.0
+Requires-Dist: libigl>=2.5
+Requires-Dist: plotly>=5.0
+Requires-Dist: kaleido>=0.2.1
+
+# DenSR
+
+DenSR provides density-aware spatial randomization using KDE-weighted sampling within a 3D cell mesh, plus object-based colocalization analysis for observed RNA spot coordinates, UniSR, and DenSR.
+
+## Install
+
+```bash
+pip install .
+```
+
+## One-line use
+
+```python
+from densr import densr
+
+spots1 = "C1_1a_xyz.txt"
+spots2 = "C1_1b_xyz.txt"
+object = "C1_volume.obj"
+colocalization_threshold = 1
+
+results = densr(
+    spots1=spots1,
+    spots2=spots2,
+    object=object,
+    colocalization_threshold=colocalization_threshold,
+)
+```
+
+The RNA spot files are read as tab-separated text files, and the first three columns are used as x, y, and z coordinates.
+The `densr(...)` call displays the results table and spot plot automatically.
+
+## Built-in sample data
+
+```python
+from densr import densr, sample_data
+
+sample = sample_data()
+
+results = densr(
+    spots1=sample.spots1,
+    spots2=sample.spots2,
+    object=sample.object,
+    colocalization_threshold=0.25,
+)
+```
+
+## Command line
+
+```bash
+densr C1_volume.obj C1_1a_xyz.txt C1_1b_xyz.txt --colocalization-threshold 1
+```
+
+## Public functions
+
+- `extract_rna_spots(file)`: extract RNA spot coordinates from a text file.
+- `filter_spots_inside_mesh(mesh, spots)`: retain only spots located within the 3D cell mesh.
+- `coloc_percentage(spots1, spots2, threshold=0.5)`: calculate bidirectional object-based colocalization between two spot populations.
+- `generate_unisr_spots(mesh, desired_points)`: UniSR, uniform spatial randomization within the 3D cell mesh.
+- `generate_densr_spots(rna_spots, mesh)`: DenSR, density-aware spatial randomization using KDE-weighted sampling within the 3D cell mesh.
+- `densr(spots1, spots2, object, colocalization_threshold=1)`: one-line DenSR analysis using RNA spot files and a 3D cell mesh file.
+- `sample_data()`: return file paths for the built-in DenSR sample data.

densr-0.1.0/README.md

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+# DenSR
+
+DenSR provides density-aware spatial randomization using KDE-weighted sampling within a 3D cell mesh, plus object-based colocalization analysis for observed RNA spot coordinates, UniSR, and DenSR.
+
+## Install
+
+```bash
+pip install .
+```
+
+## One-line use
+
+```python
+from densr import densr
+
+spots1 = "C1_1a_xyz.txt"
+spots2 = "C1_1b_xyz.txt"
+object = "C1_volume.obj"
+colocalization_threshold = 1
+
+results = densr(
+    spots1=spots1,
+    spots2=spots2,
+    object=object,
+    colocalization_threshold=colocalization_threshold,
+)
+```
+
+The RNA spot files are read as tab-separated text files, and the first three columns are used as x, y, and z coordinates.
+The `densr(...)` call displays the results table and spot plot automatically.
+
+## Built-in sample data
+
+```python
+from densr import densr, sample_data
+
+sample = sample_data()
+
+results = densr(
+    spots1=sample.spots1,
+    spots2=sample.spots2,
+    object=sample.object,
+    colocalization_threshold=0.25,
+)
+```
+
+## Command line
+
+```bash
+densr C1_volume.obj C1_1a_xyz.txt C1_1b_xyz.txt --colocalization-threshold 1
+```
+
+## Public functions
+
+- `extract_rna_spots(file)`: extract RNA spot coordinates from a text file.
+- `filter_spots_inside_mesh(mesh, spots)`: retain only spots located within the 3D cell mesh.
+- `coloc_percentage(spots1, spots2, threshold=0.5)`: calculate bidirectional object-based colocalization between two spot populations.
+- `generate_unisr_spots(mesh, desired_points)`: UniSR, uniform spatial randomization within the 3D cell mesh.
+- `generate_densr_spots(rna_spots, mesh)`: DenSR, density-aware spatial randomization using KDE-weighted sampling within the 3D cell mesh.
+- `densr(spots1, spots2, object, colocalization_threshold=1)`: one-line DenSR analysis using RNA spot files and a 3D cell mesh file.
+- `sample_data()`: return file paths for the built-in DenSR sample data.

densr-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "densr"
+version = "0.1.0"
+description = "Density-aware spatial randomization and object-based colocalization analysis for 3D RNA spot data."
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "MIT" }
+authors = [
+  { name = "Sudharsan Kannan" }
+]
+dependencies = [
+  "numpy>=1.23",
+  "pandas>=1.5",
+  "scipy>=1.9",
+  "trimesh>=3.20",
+  "rtree>=1.0",
+  "libigl>=2.5",
+  "plotly>=5.0",
+  "kaleido>=0.2.1",
+]
+
+[project.scripts]
+densr = "densr.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+densr = ["sample_data/*"]

densr-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

densr-0.1.0/setup.py

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+from setuptools import setup
+
+
+setup()
+

densr-0.1.0/src/densr/__init__.py

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+"""DenSR package API."""
+
+from .analysis import (
+    DenSRResults,
+    DenSRSampleData,
+    calculate_max_density,
+    calculate_max_density_bbox,
+    coloc_percentage,
+    densr,
+    extract_rna_spots,
+    filter_spots_inside_mesh,
+    generate_densr_spots,
+    generate_unisr_spots,
+    sample_data,
+)
+
+__all__ = [
+    "DenSRResults",
+    "DenSRSampleData",
+    "calculate_max_density",
+    "calculate_max_density_bbox",
+    "coloc_percentage",
+    "densr",
+    "extract_rna_spots",
+    "filter_spots_inside_mesh",
+    "generate_densr_spots",
+    "generate_unisr_spots",
+    "sample_data",
+]