pysccdc 0.1.0__tar.gz

pysccdc-0.1.0/LICENSE

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pysccdc-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pysccdc
+Version: 0.1.0
+Summary: Pure-Python port of the R package scCDC — entropy-based, gene-specific ambient-RNA contamination detection and correction for scRNA-seq / snRNA-seq.
+Author-email: Zehua Zeng <starlitnightly@163.com>
+License: 
+                                         Apache License
+                                   Version 2.0, January 2004
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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+              other commercial damages or losses), even if such Contributor
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+           Licensed under the Apache License, Version 2.0 (the "License");
+           you may not use this file except in compliance with the License.
+           You may obtain a copy of the License at
+        
+               http://www.apache.org/licenses/LICENSE-2.0
+        
+           Unless required by applicable law or agreed to in writing, software
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+           See the License for the specific language governing permissions and
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+        
+Project-URL: Homepage, https://github.com/omicverse/py-sccdc
+Project-URL: Repository, https://github.com/omicverse/py-sccdc
+Project-URL: Issues, https://github.com/omicverse/py-sccdc/issues
+Project-URL: Upstream R package, https://github.com/ZJU-UoE-CCW-LAB/scCDC
+Project-URL: Upstream (omicverse), https://github.com/Starlitnightly/omicverse
+Keywords: scRNA-seq,snRNA-seq,ambient-RNA,contamination,decontamination,scCDC,single-cell,entropy,GCG,Youden-index,anndata
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.10
+Requires-Dist: pandas>=1.5
+Requires-Dist: anndata>=0.8
+Requires-Dist: scikit-learn>=1.1
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Dynamic: license-file
+
+# pysccdc
+
+A **pure-Python re-implementation of [scCDC](https://github.com/ZJU-UoE-CCW-LAB/scCDC)** (Wang et al., *Genome Biology* 2024) for entropy-based, **gene-specific** ambient-RNA contamination detection and correction in single-cell / single-nucleus RNA-seq data.
+
+- AnnData-native — drop-in for the scanpy / omicverse ecosystem
+- **No `rpy2`**, no R install — the Shannon-entropy core, the bootstrapped smoothing-spline curve fit, the normal-tail FDR, the AUROC and the Youden-index thresholding are all implemented directly in NumPy/SciPy
+- Same function surface as the R workflow (`ContaminationDetection` → `ContaminationQuantification` → `ContaminationCorrection`)
+- Bit-for-bit reproducibility against the R reference for the deterministic core — per-gene/per-cluster entropy and the corrected count matrix match scCDC exactly (see `tests/test_r_parity.py`)
+
+Unlike DecontX, SoupX, CellBender or scAR — which correct *every* gene — scCDC detects the small set of **Global Contamination-causing Genes (GCGs)** and corrects only those, avoiding the over-correction of lowly / non-contaminating genes (many of which are real cell-type markers). It needs **no empty-droplet data**.
+
+> This is a **standalone mirror** of the canonical implementation that lives in [`omicverse`](https://github.com/Starlitnightly/omicverse). All algorithmic work is developed upstream in omicverse and synced here for users who want scCDC without the full omicverse stack.
+
+## Install
+
+```bash
+pip install pysccdc
+```
+
+or, from a checkout:
+
+```bash
+pip install -e .
+```
+
+Dependencies: `numpy`, `scipy`, `pandas`, `anndata`, `scikit-learn`. No R, no `rpy2`.
+
+## How it works
+
+1. **Observed entropy** — for every gene in every cell cluster, compute the Shannon entropy (base 2) of its count distribution across droplets. A gene smeared across many droplets at a near-constant low ambient level has a *concentrated* count distribution → low entropy.
+2. **Expected entropy curve** — fit the expected entropy as a smooth function of `log1p(mean expression)` with a bootstrapped, outlier-trimmed smoothing spline learnt from presumed-clean genes.
+3. **Entropy divergence** = expected − observed entropy. A gene with significant positive divergence (normal-tail p, FDR ≤ 0.05) in more than `restriction_factor` of clusters — and expressed in enough cells in every cluster — is flagged a **GCG**.
+4. **Gene-specific correction** — for each GCG, rank clusters by log-normalized expression, compute per-cluster **AUROC** vs the lowest-expressing cluster, split into eGCG-positive / -negative, then take the **Youden-index** count threshold on the pooled count distributions and subtract `round(threshold)` (floored at zero). **Non-GCG genes are left untouched** — scCDC's anti-over-correction design.
+
+## Quick-start
+
+```python
+import pysccdc as cd
+
+# bundled synthetic dataset: 4 clusters x 200 cells, 120 genes,
+# 4 deliberately-spiked contaminating genes
+adata = cd.datasets.simulate_contaminated(random_state=0)
+
+# 1) detect GCGs
+detection = cd.ContaminationDetection(adata, cluster_key="cluster")
+detection                       # degree-of-contamination table (GCGs)
+detection.attrs["GCGs"]         # the GCG list
+
+# 2) quantify dataset-level contamination
+ratio = cd.ContaminationQuantification(adata, detection,
+                                       cluster_key="cluster")
+
+# 3) correct only the GCGs
+corrected = cd.ContaminationCorrection(adata, detection,
+                                       cluster_key="cluster")
+corrected.layers["Corrected"]          # decontaminated count matrix
+corrected.uns["sccdc"]["thresholds"]   # per-GCG subtraction thresholds
+```
+
+scCDC works on a **filtered, clustered** count matrix; any AnnData with raw integer counts in `.X` (or a named `layer`) and a categorical cluster label in `.obs` works. See `examples/tutorial_standalone.py` for an end-to-end run on the bundled clustered PBMC 3k dataset (`data/pbmc3k_clustered.h5ad`).
+
+## Low-level functional API (mirrors R one-to-one)
+
+```python
+from pysccdc import (
+    ContaminationDetection, ContaminationQuantification, ContaminationCorrection,
+    generate_curve, vector_entropy, matrix_entropy,
+    SmoothSpline, smooth_spline, simple_roc, youden_threshold,
+)
+
+# Shannon entropy of a single gene's count distribution
+matrix_entropy(counts_genes_by_cells)        # one entropy per gene
+
+# Fit one cluster's entropy-vs-expression curve directly
+generate_curve(df_with_Gene_meanexpr_entropy, spar=1.0)
+
+# AUROC and the Youden-index cut point
+simple_roc(expr, cls)
+youden_threshold(neg_counts, pos_counts)
+```
+
+## What's included
+
+| Python | R counterpart | Purpose |
+|---|---|---|
+| `ContaminationDetection` | `ContaminationDetection` | detect GCGs; per-cluster entropy divergence table |
+| `ContaminationQuantification` | `ContaminationQuantification` | dataset-level contamination ratio from the GCGs |
+| `ContaminationCorrection` | `ContaminationCorrection` | Youden-threshold correction of the GCGs only |
+| `generate_curve` | `generate_curve` | fit one cluster's entropy-vs-expression curve |
+| `vector_entropy` / `matrix_entropy` | `VectorToEntropy` / `MatrixToEntropy` | Shannon entropy of count distributions |
+| `SmoothSpline` / `smooth_spline` | `smooth.spline` | penalized cubic B-spline |
+| `simple_roc` / `youden_threshold` | `simple_roc` / `Cal_thres` | AUROC and Youden-index cut point |
+| `datasets.simulate_contaminated` | — | synthetic clustered counts with spiked GCGs |
+
+## Reproducing R results exactly
+
+`tests/` runs the **same** synthetic dataset through the R package scCDC 1.4 (`tests/r_reference_driver.R`) and `pysccdc`, and asserts agreement:
+
+* **per-gene / per-cluster Shannon entropy — bit-exact** (the Rcpp `MatrixToEntropy` reduces to a deterministic `numpy.bincount`);
+* **detected GCG list — identical** on the deliberately-spiked synthetic dataset;
+* **corrected count matrix — bit-exact** (the Youden-threshold path is fully deterministic);
+* **contamination ratio — bit-exact**;
+* **per-gene entropy divergence — Pearson r > 0.99**.
+
+**Unavoidable difference.** The entropy-vs-expression curve is fit by a *bootstrapped* smoothing spline (10 rounds, 80% gene resampling). Two things differ from R: (i) R's `sample()` (Mersenne-Twister) and NumPy's PCG64 draw different bootstrap subsets, and (ii) R's `smooth.spline` uses an internal knot-thinning heuristic and GCV machinery that the scipy penalized cubic B-spline reproduces only up to ~1e-3 in entropy units. These propagate into the entropy *divergence* (hence r > 0.99 rather than bit-exact), and on a real noisy dataset can move a few borderline genes across the FDR cutoff in the GCG list — but **not** into the corrected matrix, which matches exactly given the same GCG list. Fix `random_state` for reproducible Python runs. The `examples/compare_R_vs_Python.ipynb` notebook demonstrates this on real PBMC 3k data.
+
+## Examples
+
+`examples/` mirrors the reference layout:
+
+* `r_driver_sccdc.R` — drives R scCDC end-to-end, dumps entropy / GCG / distance / corrected-matrix outputs
+* `compare_R_vs_Python.ipynb` (+ `.executed.ipynb`) — runs R scCDC via `Rscript` and `pysccdc` on the bundled clustered PBMC 3k dataset and visualizes the agreement (entropy bit-exact, divergence correlation, GCG-set Venn, bit-exact corrected matrix) via `omicverse.pl.*`
+* `tutorial_standalone.py` — minimal end-to-end pysccdc pipeline
+* `benchmark.py` — head-to-head speed comparison
+
+## Relationship to omicverse
+
+Developed **upstream** in [`omicverse`](https://github.com/Starlitnightly/omicverse):
+
+- Canonical implementation: omicverse single-cell decontamination
+- Standalone mirror (this repo): same code, same API, minus the omicverse packaging
+
+## Citation
+
+If you use this package, please cite the original scCDC paper:
+
+> Wang, W. *et al.* **scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data.** *Genome Biology* **25**, 122 (2024).
+
+and acknowledge omicverse / this repo for the Python port.
+
+## License
+
+Apache-2.0. The upstream R package scCDC is GPL (≥ 2); `pysccdc` is an independent re-implementation from the published algorithm and the scCDC source.