annotuneagent 0.1.0__py3-none-any.whl

annotuneagent-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: annotuneagent
+Version: 0.1.0
+Summary: Cluster-level cell-type annotation from marker, name, and ML results
+Author-email: "Zhao Li (李钊)" <leelieber@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/leelieber2025/AnnoTuneAgent
+Project-URL: Documentation, https://app.readthedocs.org/projects/annotuneagent/
+Project-URL: Changelog, https://github.com/leelieber2025/AnnoTuneAgent/blob/main/CHANGELOG.md
+Project-URL: Source, https://github.com/leelieber2025/AnnoTuneAgent
+Project-URL: Issues, https://github.com/leelieber2025/AnnoTuneAgent/issues
+Project-URL: PyPI, https://pypi.org/project/annotuneagent/
+Keywords: single-cell,RNA-seq,cell type annotation,marker genes,bioinformatics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: anndata>=0.11.3
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=1.4
+Requires-Dist: scipy>=1.7
+Requires-Dist: scanpy[leiden]>=1.10
+Requires-Dist: scikit-misc>=0.1.4
+Requires-Dist: numba>=0.57
+Requires-Dist: scikit-learn>=1.1
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: pyyaml>=6
+Provides-Extra: scvi
+Requires-Dist: scvi-tools>=1.1.3; extra == "scvi"
+Provides-Extra: models
+Requires-Dist: transformers; extra == "models"
+Provides-Extra: scfair
+Requires-Dist: scfair>=0.8; extra == "scfair"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff<0.17,>=0.4.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0; extra == "docs"
+Requires-Dist: sphinx-book-theme>=1.1; extra == "docs"
+Requires-Dist: myst-nb>=1.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5; extra == "docs"
+Requires-Dist: sphinx-design>=0.5; extra == "docs"
+Dynamic: license-file
+
+# AnnoTuneAgent
+
+[![License](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/annotuneagent.svg)](https://pypi.org/project/annotuneagent/)
+[![Documentation](https://app.readthedocs.org/projects/annotuneagent/badge/?version=latest)](https://app.readthedocs.org/projects/annotuneagent/)
+
+Documentation: [Read the Docs](https://app.readthedocs.org/projects/annotuneagent/).
+
+**Cluster-level cell-type annotation for single-cell RNA-seq, with two
+fine-tuned language models that run locally.**
+
+Each cluster gets a marker score, a name-model result, and an ML-model
+result. A rule-based judgment reads all three and writes the title, so every
+call stays auditable.
+
+## What is fine-tuned
+
+One Qwen3.5-4B base (Q6_K GGUF) is shared by two independent LoRA adapters.
+The adapters are not merged into the base, so they load together on a single
+local `llama-server` and can be replaced without touching the base.
+
+| Model | Task it was fine-tuned for | Input | Output |
+| --- | --- | --- | --- |
+| **name** | Choose a cell-type name from the marker dictionary | Cluster marker evidence and `dictionary_hits` | A name copied from `dictionary_hits` when that type's markers support the cluster |
+| **ML** | Choose a name from measured cluster statistics | Differential expression, candidate marker panels, log fold change, fraction of cells expressing each gene inside and outside the cluster, panel summaries | A name copied from those candidates |
+
+Both models are trained to **copy** a name from the candidates they are
+shown, not to free-write one. A name outside the candidate list cannot become
+a title, and a name with no marker that passes expression and specificity
+validation is flagged (`no_marker_passed`) instead of being trusted silently.
+
+The weights are on the Hugging Face Hub:
+[lieberlee/annotune-qwen3.5-4b-gguf](https://huggingface.co/lieberlee/annotune-qwen3.5-4b-gguf)
+(preview). Inference is local: no cluster data leaves the machine.
+
+## Pipeline
+
+```text
+raw counts ─ prepare ─▶ QC, doublets, normalization, batch correction, Leiden
+           ─ run ─────▶ per cluster:
+                          1. marker score        (built-in human / mouse dictionary)
+                          2. name model          (LoRA, copies from dictionary_hits)
+                          3. ML model            (LoRA, copies from measured candidates)
+                          ▼
+                        judgment ─▶ title + status + reason + hint
+                          ▼
+                        validated marker panels, dotplot, report, annotated h5ad
+```
+
+- **Judgment, not voting.** Agreement among the three results gives a clear
+  title. Disagreement, mixed programs, and unvalidated names are kept and
+  flagged with a reason (`mixed_programs`, `near_clear_cluster`,
+  `subcluster_labels`, `no_marker_passed`) so you can review them.
+- **Marker evidence is checked, not quoted.** Panels are selected from cited
+  dictionary markers and validated against measured expression and
+  specificity in your data.
+- **Every title is traceable.** The report records each model's answer, the
+  panel, and the reason a cluster was or was not settled.
+
+The models run when `models` is passed (or the CLI adapter flags are given).
+Without them, `run` uses the marker score alone.
+
+## Install
+
+Python 3.10–3.13.
+
+```bash
+pip install annotuneagent
+```
+
+Local GGUF models need `pip install 'annotuneagent[models]'`. Optional methods:
+AmbiDose (`denoise=True`, [install](https://github.com/leelieber2025/AmbiDose)),
+scVI and SOLO (`annotuneagent[scvi]`), scFair (`annotuneagent[scfair]`),
+Harmony, and Scanorama. If you select one that is missing, `prepare` prints
+the install command and leaves the matrix unchanged. See
+[Installation](docs/installation.md).
+
+From a checkout: `pip install -e '.[dev]'`.
+
+## First run
+
+`prepare` expects raw integer counts. `run` expects finite, nonnegative,
+library-size-normalized natural log1p expression with Scanpy's
+`adata.uns["log1p"]`, which `prepare` writes.
+
+```python
+import annotuneagent as ata
+
+adata = ata.read_10x("outs", ["sample_a", "sample_b"])
+adata = ata.prepare(adata, species="human", batch_key="sample")
+report = ata.run(adata, "leiden", species="human", subcluster=False)
+```
+
+`read_10x` takes one filtered matrix per sample folder (`*.h5`, or the mtx
+directory when there is no h5). Scrublet and SOLO run per sample on those
+filtered counts. `doublet_chip="10k"` (default) uses 0.8% multiplets per
+1,000 recovered cells, and `"20k"` uses 0.4%.
+
+To score a caller-supplied list instead of the built-in dictionary:
+
+```python
+records = ata.annotate(
+    adata,
+    cluster_key="leiden",
+    hypotheses=[
+        ata.Hypothesis(
+            "CD4-positive, alpha-beta T cell",
+            positive=("CD3E", "CD4"),
+            negative=("CD8A",),
+        ),
+        ata.Hypothesis(
+            "CD8-positive, alpha-beta T cell",
+            positive=("CD3E", "CD8A"),
+            negative=("CD4",),
+        ),
+    ],
+)
+```
+
+A label needs positive marker enrichment. A negative marker counts against a
+hypothesis only when the cluster is enriched for it relative to the other
+cells. Scores are operational, not probabilities.
+
+The built-in table is `markers.tsv`: human and mouse, each with a
+tissue-agnostic core and organ pages. Tissue rows stay hidden until `tissue`
+matches. Symbols are not translated across species. `evaluate` compares
+records with a per-cell author label: the reference for a cluster is the
+majority label, a tied majority is left unmatched, and a parent name counts
+as a coarse match.
+
+```bash
+annotuneagent \
+  --input clustered.h5ad \
+  --cluster-key leiden \
+  --species human \
+  --output result.json
+```
+
+`--name-adapter`, `--ml-adapter`, and `--base` run the name and ML models on
+one local server and require `--output-h5ad`. The weights are on the Hugging
+Face Hub: [lieberlee/annotune-qwen3.5-4b-gguf](https://huggingface.co/lieberlee/annotune-qwen3.5-4b-gguf).
+The tokenizer is installed with the package. See
+[docs/tutorials/load_model.ipynb](docs/tutorials/load_model.ipynb).
+
+## Status
+
+**0.1.0 (Alpha).** Import as `import annotuneagent as ata`.
+
+## License
+
+Software: [Apache License 2.0](LICENSE).
+
+## Author
+
+**Zhao Li (李钊)**
+Email: [leelieber@gmail.com](mailto:leelieber@gmail.com)

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annotuneagent-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+annotuneagent = annotuneagent.cli:main

annotuneagent-0.1.0.dist-info/licenses/LICENSE

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annotuneagent-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+annotuneagent