shanuz 0.1.1__tar.gz

shanuz-0.1.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Create venv and install
+        run: |
+          uv venv --python ${{ matrix.python-version }}
+          uv pip install -e ".[all]"
+
+      - name: Lint (ruff, advisory)
+        # Pre-existing lint debt in older modules is not yet cleared, so the
+        # full check is informational; it must not gate the build.
+        run: uv run ruff check shanuz || true
+
+      - name: Run tests
+        run: uv run pytest tests/ -q

shanuz-0.1.1/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+*.egg
+*.egg-info/
+dist/
+build/
+.eggs/
+
+# Virtual environments (uv)
+.venv/
+venv/
+env/
+
+# uv
+.uv/
+uv.lock
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# Data cache
+shanuz_data/
+~/.shanuz_data/
+
+# OS
+.DS_Store
+Thumbs.db

shanuz-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Shanika Amarasoma
+
+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.

shanuz-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: shanuz
+Version: 0.1.1
+Summary: Python single-cell genomics toolkit — a port of Seurat's core data structures and analysis pipeline
+Project-URL: Homepage, https://github.com/GenomicAI/shanuz
+Project-URL: Repository, https://github.com/GenomicAI/shanuz
+Project-URL: Bug Tracker, https://github.com/GenomicAI/shanuz/issues
+Author-email: Shanika Amarasoma <shanika.amarasoma@gmail.com>
+License: MIT
+License-File: LICENSE
+Keywords: RNA-seq,bioinformatics,genomics,scRNA-seq,single-cell
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+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: >=3.10
+Requires-Dist: numpy>=1.24
+Requires-Dist: packaging>=23.0
+Requires-Dist: pandas>=2.0
+Requires-Dist: scipy>=1.10
+Provides-Extra: all
+Requires-Dist: anndata>=0.10; extra == 'all'
+Requires-Dist: build; extra == 'all'
+Requires-Dist: leidenalg>=0.10; extra == 'all'
+Requires-Dist: matplotlib>=3.7; extra == 'all'
+Requires-Dist: numba>=0.59; extra == 'all'
+Requires-Dist: pytest-cov; extra == 'all'
+Requires-Dist: pytest>=7; extra == 'all'
+Requires-Dist: python-igraph>=0.11; extra == 'all'
+Requires-Dist: ruff; extra == 'all'
+Requires-Dist: scikit-learn>=1.3; extra == 'all'
+Requires-Dist: scikit-misc>=0.3; extra == 'all'
+Requires-Dist: seaborn>=0.12; extra == 'all'
+Requires-Dist: statsmodels>=0.14; extra == 'all'
+Requires-Dist: twine; extra == 'all'
+Requires-Dist: umap-learn>=0.5; extra == 'all'
+Provides-Extra: analysis
+Requires-Dist: leidenalg>=0.10; extra == 'analysis'
+Requires-Dist: matplotlib>=3.7; extra == 'analysis'
+Requires-Dist: numba>=0.59; extra == 'analysis'
+Requires-Dist: python-igraph>=0.11; extra == 'analysis'
+Requires-Dist: scikit-learn>=1.3; extra == 'analysis'
+Requires-Dist: scikit-misc>=0.3; extra == 'analysis'
+Requires-Dist: seaborn>=0.12; extra == 'analysis'
+Requires-Dist: statsmodels>=0.14; extra == 'analysis'
+Requires-Dist: umap-learn>=0.5; extra == 'analysis'
+Provides-Extra: anndata
+Requires-Dist: anndata>=0.10; extra == 'anndata'
+Provides-Extra: dev
+Requires-Dist: build; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest>=7; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: twine; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# Shanuz — Python Single-Cell Genomics Toolkit
+
+[![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+**Shanuz** is a Python port of the [Seurat](https://satijalab.org/seurat/) single-cell RNA-seq
+analysis framework, implementing Seurat's core data structures, preprocessing pipeline,
+dimensionality reduction, clustering, and marker detection — entirely in Python.
+
+> The package is spiritually and algorithmically faithful to Seurat v5 while providing a
+> pure-Python, pip-installable alternative that integrates naturally with NumPy, SciPy,
+> and AnnData ecosystems.
+
+---
+
+## Features
+
+- **Shanuz object** — mirrors the R `Seurat` S4 class with `__slots__`-based Python classes
+- **Assay5** — sparse-matrix-backed multi-layer assay (counts, data, scale.data)
+- **Preprocessing** — `normalize_data`, `find_variable_features` (VST), `scale_data`, `percentage_feature_set`
+- **SCTransform** — `sctransform` (regularized negative-binomial Pearson residuals)
+- **Signature scoring** — `add_module_score`, `cell_cycle_scoring` (S/G2M + Phase)
+- **Dimensionality reduction** — `run_pca` (via scikit-learn)
+- **Nearest-neighbour graph** — `find_neighbors` (KNN + SNN)
+- **Clustering** — `find_clusters` (Louvain via python-igraph, Leiden via leidenalg)
+- **UMAP** — `run_umap` (via umap-learn)
+- **PC significance** — `jack_straw`, `score_jackstraw` (JackStraw permutation test)
+- **Differential expression** — `find_markers`, `find_all_markers` (`wilcox` tie-corrected, `t`, `LR`, `negbinom`, `roc`)
+- **Plotting** — `dim_plot`, `feature_plot`, `vln_plot`, `dot_plot`, `elbow_plot`, `do_heatmap`, `dim_heatmap`, `feature_scatter`, `variable_feature_plot`, `ridge_plot` (matplotlib/seaborn)
+- **AnnData interoperability** — `as_anndata`, `from_anndata`
+- **Spatial (Xenium / Visium / CosMx)** — `load_xenium`/`load_visium`/`load_cosmx`, `get_tissue_coordinates`, `nearest_neighbor_distance`, `local_neighborhood`, `build_niche_assay`, `composition_test`, `image_dim_plot`, `image_feature_plot`
+- **PBMC 3k tutorial** — end-to-end validated against the official Seurat tutorial
+- **PBMC 8k advanced tutorial** — larger dataset + T/NK subclustering workflow
+- **CITE-seq multimodal tutorial** — RNA + surface protein (ADT) with CLR normalization
+- **Xenium spatial tutorial** — spatial neighbourhood/niche analysis, verified to 8 s.f. against R Seurat
+
+---
+
+## Installation
+
+Shanuz is not yet published to PyPI. Install directly from the GitHub repository.
+
+### With uv (recommended)
+
+```bash
+# Install uv if you haven't already
+curl -LsSf https://astral.sh/uv/install.sh | sh  # macOS/Linux
+# or: powershell -c "irm https://astral.sh/uv/install.ps1 | iex"  # Windows
+
+git clone https://github.com/GenomicAI/shanuz.git
+cd shanuz
+uv venv
+source .venv/bin/activate   # Windows: .venv\Scripts\activate
+uv pip install -e ".[analysis]"
+```
+
+### With pip
+
+```bash
+git clone https://github.com/GenomicAI/shanuz.git
+cd shanuz
+pip install -e ".[analysis]"
+```
+
+### Full development installation (includes tests and linting)
+
+```bash
+git clone https://github.com/GenomicAI/shanuz.git
+cd shanuz
+uv venv
+source .venv/bin/activate   # Windows: .venv\Scripts\activate
+uv pip install -e ".[all]"
+```
+
+---
+
+## Quick Start
+
+```python
+import scipy.sparse as sp
+import numpy as np
+from shanuz import create_shanuz_object
+
+# Create a Shanuz object from a counts matrix
+counts = sp.random(2000, 500, density=0.2, format="csc")
+sobj = create_shanuz_object(counts, project="my_project", min_cells=3, min_features=200)
+print(sobj)
+# Shanuz object — my_project
+#   500 cells × 2000 features
+#   Active assay: 'RNA'
+#   Reductions: []
+#   Version: 5.4.0
+
+# Access metadata
+print(sobj.meta_data.head())
+```
+
+---
+
+## Tutorials
+
+Three end-to-end tutorials — from basic guided clustering to multimodal CITE-seq —
+each pairing R Seurat code side-by-side with the Python Shanuz equivalent.
+See **[`tutorials/README.md`](tutorials/README.md)** for the full index.
+
+| # | Tutorial | Dataset | Complexity |
+|---|----------|---------|-----------|
+| 1 | [PBMC 3k — Guided Clustering](tutorials/pbmc3k_tutorial.md) | 3k PBMCs · 10x Genomics | Beginner |
+| 2 | [PBMC 8k — Advanced Subclustering](tutorials/advanced_pbmc8k_subclustering.md) | 8k PBMCs · GRCh38 | Intermediate |
+| 3 | [CBMC CITE-seq — Multimodal](tutorials/multimodal_citeseq.md) | 8,600 CBMCs · RNA + 13 proteins | Advanced |
+| 4 | [PBMC 3k — SCTransform](tutorials/sctransform_vignette.md) | 3k PBMCs · 10x Genomics | Advanced |
+| 5 | [Xenium — Spatial (R vs Python)](tutorials/xenium_spatial_tutorial.md) | 36k cells · 10x Xenium mouse brain | Spatial |
+
+```bash
+# Tutorial 1 — PBMC 3k
+python tutorials/pbmc3k_tutorial.py && python tutorials/generate_plots.py
+
+# Tutorial 2 — PBMC 8k subclustering
+python tutorials/pbmc8k_subclustering_tutorial.py && python tutorials/generate_advanced_plots.py
+
+# Tutorial 3 — CITE-seq multimodal
+python tutorials/cbmc_citeseq_tutorial.py && python tutorials/generate_multimodal_plots.py
+
+# Tutorial 4 — SCTransform
+python tutorials/pbmc3k_sctransform_tutorial.py && python tutorials/generate_sctransform_plots.py
+
+# Tutorial 5 — Xenium spatial (auto-downloads ~20 MB)
+python tutorials/generate_spatial_plots.py
+```
+
+---
+
+## API Reference
+
+### Object creation
+
+```python
+from shanuz import create_shanuz_object
+
+pbmc = create_shanuz_object(
+    counts,             # scipy.sparse CSC/CSR or numpy ndarray (genes × cells)
+    project="pbmc3k",
+    min_cells=3,        # filter genes present in fewer than N cells
+    min_features=200,   # filter cells with fewer than N detected genes
+)
+```
+
+### Preprocessing
+
+```python
+from shanuz.preprocessing import (
+    normalize_data,
+    find_variable_features,
+    scale_data,
+    percentage_feature_set,
+)
+
+percentage_feature_set(pbmc, pattern=r"^MT-", col_name="percent.mt")
+normalize_data(pbmc, normalization_method="LogNormalize", scale_factor=10000)
+find_variable_features(pbmc, selection_method="vst", nfeatures=2000)
+scale_data(pbmc)
+```
+
+### Dimensionality reduction & clustering
+
+```python
+from shanuz.reduction import run_pca
+from shanuz.neighbors import find_neighbors
+from shanuz.clustering import find_clusters
+from shanuz.umap import run_umap
+
+run_pca(pbmc, n_pcs=50)
+find_neighbors(pbmc, dims=range(10), k_param=20)
+find_clusters(pbmc, resolution=0.5)
+run_umap(pbmc, dims=range(10))
+```
+
+### Differential expression
+
+```python
+from shanuz.markers import find_markers, find_all_markers
+
+markers = find_markers(pbmc, ident_1=1)
+all_markers = find_all_markers(pbmc, only_pos=True, logfc_threshold=0.25)
+```
+
+### Plotting
+
+All plotting functions return a `matplotlib.figure.Figure` — save or display as needed.
+
+```python
+from shanuz.plotting import (
+    dim_plot,            # DimPlot   — cells on UMAP/PCA coloured by ident
+    feature_plot,        # FeaturePlot — gene expression on embedding
+    vln_plot,            # VlnPlot   — violin plots per cluster
+    elbow_plot,          # ElbowPlot — stdev per PC
+    feature_scatter,     # FeatureScatter — two features vs each other
+    variable_feature_plot, # VariableFeaturePlot — mean-variance HVG plot
+    dim_heatmap,         # DimHeatmap — top loading genes per PC
+    do_heatmap,          # DoHeatmap  — expression heatmap sorted by cluster
+    ridge_plot,          # RidgePlot  — ridgeline plots per cluster
+)
+
+# Quick examples
+fig = dim_plot(pbmc, reduction="umap", label=True)
+fig = feature_plot(pbmc, ["LYZ", "MS4A1", "NKG7"], reduction="umap", ncol=3)
+fig = vln_plot(pbmc, ["LYZ", "CD3D", "PPBP"], group_by=None)
+fig = elbow_plot(pbmc, ndims=20)
+fig = do_heatmap(pbmc, top_marker_genes)
+fig.savefig("output.png", dpi=150, bbox_inches="tight")
+```
+
+| Shanuz function | R Seurat equivalent |
+|-----------------|---------------------|
+| `dim_plot` | `DimPlot` |
+| `feature_plot` | `FeaturePlot` |
+| `vln_plot` | `VlnPlot` |
+| `dot_plot` | `DotPlot` |
+| `elbow_plot` | `ElbowPlot` |
+| `feature_scatter` | `FeatureScatter` |
+| `variable_feature_plot` | `VariableFeaturePlot` |
+| `dim_heatmap` | `DimHeatmap` |
+| `do_heatmap` | `DoHeatmap` |
+| `ridge_plot` | `RidgePlot` |
+
+---
+
+## Data Structures
+
+```
+Shanuz
+├── assays: dict[str, Assay5]
+│   └── "RNA"
+│       ├── layers["counts"]    # raw integer counts (genes × cells)
+│       ├── layers["data"]      # log-normalized (genes × cells)
+│       └── layers["scale.data"] # z-scored (genes × cells)
+├── meta_data: pd.DataFrame     # per-cell metadata
+├── reductions: dict
+│   ├── "pca": DimReduc         # PCA embeddings + loadings
+│   └── "umap": DimReduc        # UMAP embeddings
+├── graphs: dict
+│   ├── "RNA_nn": Graph         # KNN graph
+│   └── "RNA_snn": Graph        # SNN graph
+└── commands: list[ShanuzCommand]  # audit log
+```
+
+---
+
+## Roadmap
+
+See **[`ROADMAP.md`](ROADMAP.md)** for the full development plan. Upcoming milestones:
+
+| Milestone | Focus |
+|-----------|-------|
+| v0.2.0 | Batch correction — Harmony, CCA/RPCA, `IntegrateLayers` |
+| v0.3.0 | Reference mapping — `FindTransferAnchors`, `TransferData`, `MapQuery` |
+| v0.4.0 | Multimodal WNN — `FindMultiModalNeighbors`, joint UMAP/clustering |
+| v0.5.0 | Additional reductions — t-SNE, ICA, SPCA, GLM-PCA |
+| v0.6.0 | Pseudobulk DE — `AggregateExpression`, DESeq2, MAST, `FindConservedMarkers` |
+| v0.7.0 | Spatial — Xenium/Visium/CosMx loaders, niche/neighbourhood analysis, `image_*` plots ✅ *(largely delivered — see Tutorial 5)*; remaining: MERSCOPE loader, `FindSpatiallyVariableFeatures` (Moran's I), Visium tissue-image plots |
+| v0.8.0 | Scale — BPCells-style lazy matrices, `SketchData`, `ProjectData` |
+| v0.9.0 | Specialized — `HTODemux`, Mixscape (CRISPR screens) |
+| v0.10.0 | Infrastructure — PyPI, GitHub Actions CI, type annotations, MkDocs site |
+
+---
+
+## Running Tests
+
+```bash
+uv pip install -e ".[dev]"
+pytest tests/ -v
+```
+
+All 144 unit tests pass.
+
+---
+
+## Dependencies
+
+| Package | Purpose |
+|---------|---------|
+| numpy, scipy, pandas | Core numerics and data frames |
+| statsmodels | LOESS smoothing for VST |
+| scikit-learn | PCA |
+| umap-learn | UMAP embedding |
+| python-igraph | Louvain clustering |
+| leidenalg | Leiden clustering |
+| packaging | Version handling |
+
+---
+
+## Credits
+
+**Development assistance:** This package was developed with the help of
+[Claude](https://claude.ai) (Anthropic's AI assistant, claude-sonnet-4-6),
+which assisted in porting the R Seurat codebase to Python, implementing
+the VST algorithm, degree-2 LOESS, Louvain clustering, and validating
+results against the official PBMC 3k tutorial.
+
+**Original R Seurat package:**  
+The algorithms and data structures in Shanuz are direct Python translations of the
+R [Seurat](https://satijalab.org/seurat/) package by the Satija Lab.
+Please cite the original Seurat papers if you use Shanuz in published work:
+
+> Hao Y, Stuart T, Kowalski MH, et al. (2024).
+> **Dictionary learning for integrative, multimodal and scalable single-cell analysis.**
+> *Nature Biotechnology*, 42, 293–304.
+> https://doi.org/10.1038/s41587-023-01767-y
+
+> Hao Y, Hao S, Andersen-Nissen E, et al. (2021).
+> **Integrated analysis of multimodal single-cell data.**
+> *Cell*, 184(13), 3573–3587.
+> https://doi.org/10.1016/j.cell.2021.04.048
+
+> Stuart T, Butler A, Hoffman P, et al. (2019).
+> **Comprehensive Integration of Single-Cell Data.**
+> *Cell*, 177(7), 1888–1902.
+> https://doi.org/10.1016/j.cell.2019.05.031
+
+> Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. (2018).
+> **Integrating single-cell transcriptomic data across different conditions, technologies, and species.**
+> *Nature Biotechnology*, 36, 411–420.
+> https://doi.org/10.1038/nbt.4096
+
+**PBMC 3k dataset:**  
+10x Genomics. (2016). *3k PBMCs from a Healthy Donor*.
+https://www.10xgenomics.com/resources/datasets/3-k-pb-mcs-from-a-healthy-donor-1-standard-1-1-0
+
+---
+
+## License
+
+MIT License — see [LICENSE](LICENSE) for details.
+
+This software is an independent reimplementation for educational and research purposes.
+It is not affiliated with, endorsed by, or maintained by the Satija Lab or 10x Genomics.