hide-deconv 0.1.0__tar.gz

hide_deconv-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Dennis Voelkl
+
+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.

hide_deconv-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hide-deconv
+Version: 0.1.0
+Summary: HIDE-Deconv - Hierarchical Cell Type Deconvolution
+License-Expression: MIT
+License-File: LICENSE
+Author: Dennis Voelkl
+Author-email: dennis.k.volkl@uib.no
+Requires-Python: >=3.12,<3.15
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: anndata (>=0.12.10,<0.13.0)
+Requires-Dist: click (>=8.3.2,<9.0.0)
+Requires-Dist: cvxpy (>=1.8.2,<2.0.0)
+Requires-Dist: gurobipy (>=13.0.1,<14.0.0)
+Requires-Dist: inquirerpy (>=0.3.4,<0.4.0)
+Requires-Dist: lifelines (>=0.30.3,<0.31.0)
+Requires-Dist: numpy (>=2.4.4,<3.0.0)
+Requires-Dist: pandas (>=2.3.3,<3.0.0)
+Requires-Dist: requests (>=2.33.1,<3.0.0)
+Requires-Dist: rich (>=14.3.3,<15.0.0)
+Requires-Dist: scanpy (>=1.12.1,<2.0.0)
+Requires-Dist: scikit-learn (>=1.8.0,<2.0.0)
+Requires-Dist: scikit-posthocs (>=0.12.0,<0.13.0)
+Requires-Dist: scipy (>=1.17.1,<2.0.0)
+Requires-Dist: seaborn (>=0.13.2,<0.14.0)
+Requires-Dist: torch (>=2.11.0,<3.0.0)
+Project-URL: Homepage, https://github.com/dvoelkl/HIDE-deconv
+Project-URL: Issues, https://github.com/dvoelkl/HIDE-deconv/issues
+Project-URL: Repository, https://github.com/dvoelkl/HIDE-deconv
+Description-Content-Type: text/markdown
+
+# HIDE-deconv
+
+**Interactive command line tool and python package for hierarchical deconvolution and analysis of bulk RNA-seq data.**
+
+---
+
+## Features
+
+- Designed for AnnData single cell datasets
+- Open Source package, that can be run on safe servers
+- Hierarchical cell type deconvolution for any number of cell type annotation layers
+- Includes methods for post-deconvolution analysis
+- Usable via command line interface and Python API
+- Provides a guided workflow that allows users without programming experience to perform deconvolution
+
+## Installation
+
+```bash
+# Create and activate a new virtual environment (recommended)
+python3 -m venv .venv
+source .venv/bin/activate
+
+# Install HIDE-deconv
+pip install hide-deconv
+```
+
+---
+
+## Necessary Data
+
+- **Single-cell data:** Annotated AnnData (.h5ad) file with gene names in `adata.var_names` and cell type annotations for each desired layer in `adata.obs` (at least one layer of cell type annotations is necessary).
+- **Bulk RNA-seq data:** CSV file, genes as row index, samples as columns. Gene IDs must match single-cell data.
+- **Sample sheet (optional):** CSV with sample meta-information (e.g., cohort, survival time, event).
+- **Data Normalization:** We recommend to use raw counts for all datasets.
+
+---
+
+## Command Line Workflow
+
+**Deconvolution (standard workflow):**
+```bash
+hide-deconv run --path <project_dir>
+```
+This initializes the project, preprocesses data, trains the model, and runs deconvolution.
+
+**Difference in composition & survival analysis:**
+```bash
+hide-deconv analyze diff --path <project_dir>
+hide-deconv analyze survival --path <project_dir>
+```
+- For difference analysis, the sample sheet must contain columns for sample ID and cohort.
+- For survival analysis, the sample sheet must contain columns for sample ID, survival time, and event.
+
+**Command overview:**
+```bash
+hide-deconv help
+```
+
+This displays a short introduction to the command line interface and gives an overview of all available commands.
+
+---
+
+## API Example
+
+```python
+import anndata as ad
+import pandas as pd
+import numpy as np
+from hide_deconv.preprocessing import (
+	train_test_split_adata,
+	create_reference,
+	create_hierarchy,
+	create_bulks,
+)
+from hide_deconv.models import HIDE
+from hide_deconv.statistic import run_mann_whitney_u
+
+# 1. Load AnnData
+adata = ad.read_h5ad("single_cells.h5ad")
+
+# 2. Split into training and test set
+adata_train, adata_test = train_test_split_adata(adata, celltype_col="cell_type", train_frac=0.7)
+
+# 3. Create reference profiles and hierarchy (single layer example)
+X_sub = create_reference(adata_train, celltype_col="cell_type")
+A_l = [pd.DataFrame(np.eye(X_sub.shape[1]), index=X_sub.columns, columns=X_sub.columns)]
+X_l = [X_sub]
+
+# 4. Simulate training bulks
+Y_train, C_train = create_bulks(adata_train, n_bulks=1000, n_cells_per_bulk=100, celltype_col="cell_type")
+
+# 5. Simulate test bulks
+Y_test, C_test = create_bulks(adata_test, n_bulks=100, n_cells_per_bulk=100, celltype_col="cell_type")
+
+# 6. Initialize and train model
+hide = HIDE(X_l, A_l)
+hide.train(Y_train, C_train, iter=1000)
+
+# 7. Deconvolution on test data
+results = hide.predict(Y_test, norm=True)["prediction"]
+
+# 8. Optional: Difference in composition analysis
+# (requires a sample sheet with columns 'SampleID' and 'Cohort')
+
+# sample_sheet = read_csv("sample_sheet.csv")
+# diff = run_mann_whitney_u(results[0], sample_sheet, sample_id_col="SampleID", cohort_col="Cohort")
+```
+
+---
+
+## Citation
+HIDE-deconv's deconvolution algorithm is based on HIDE: Hierarchical Cell Type Deconvolution. If you use HIDE-deconv, please cite the following article.
+
+Dennis Völkl, Malte Mensching-Buhr, Thomas Sterr, Sarah Bolz, Andreas Schäfer, Nicole Seifert, Jana Tauschke, Austin Rayford, Oddbjørn Straume, Helena U Zacharias, Sushma Nagaraja Grellscheid, Tim Beissbarth, Michael Altenbuchinger, Franziska Görtler, HIDE: hierarchical cell-type deconvolution, Bioinformatics, Volume 41, Issue Supplement_1, July 2025, Pages i207–i216, https://doi.org/10.1093/bioinformatics/btaf179
+
+---
+
+## License
+
+This project is licensed under the MIT License.
+
+---
+
+## Contact
+
+For questions, support or scientific collaboration:
+- Dennis Voelkl: dennis.k.voelkl(at)uib.no
+- Franziska Goertler: Franziska.Gortler(at)uib.no
+
+---
+

hide_deconv-0.1.0/README.md

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+# HIDE-deconv
+
+**Interactive command line tool and python package for hierarchical deconvolution and analysis of bulk RNA-seq data.**
+
+---
+
+## Features
+
+- Designed for AnnData single cell datasets
+- Open Source package, that can be run on safe servers
+- Hierarchical cell type deconvolution for any number of cell type annotation layers
+- Includes methods for post-deconvolution analysis
+- Usable via command line interface and Python API
+- Provides a guided workflow that allows users without programming experience to perform deconvolution
+
+## Installation
+
+```bash
+# Create and activate a new virtual environment (recommended)
+python3 -m venv .venv
+source .venv/bin/activate
+
+# Install HIDE-deconv
+pip install hide-deconv
+```
+
+---
+
+## Necessary Data
+
+- **Single-cell data:** Annotated AnnData (.h5ad) file with gene names in `adata.var_names` and cell type annotations for each desired layer in `adata.obs` (at least one layer of cell type annotations is necessary).
+- **Bulk RNA-seq data:** CSV file, genes as row index, samples as columns. Gene IDs must match single-cell data.
+- **Sample sheet (optional):** CSV with sample meta-information (e.g., cohort, survival time, event).
+- **Data Normalization:** We recommend to use raw counts for all datasets.
+
+---
+
+## Command Line Workflow
+
+**Deconvolution (standard workflow):**
+```bash
+hide-deconv run --path <project_dir>
+```
+This initializes the project, preprocesses data, trains the model, and runs deconvolution.
+
+**Difference in composition & survival analysis:**
+```bash
+hide-deconv analyze diff --path <project_dir>
+hide-deconv analyze survival --path <project_dir>
+```
+- For difference analysis, the sample sheet must contain columns for sample ID and cohort.
+- For survival analysis, the sample sheet must contain columns for sample ID, survival time, and event.
+
+**Command overview:**
+```bash
+hide-deconv help
+```
+
+This displays a short introduction to the command line interface and gives an overview of all available commands.
+
+---
+
+## API Example
+
+```python
+import anndata as ad
+import pandas as pd
+import numpy as np
+from hide_deconv.preprocessing import (
+	train_test_split_adata,
+	create_reference,
+	create_hierarchy,
+	create_bulks,
+)
+from hide_deconv.models import HIDE
+from hide_deconv.statistic import run_mann_whitney_u
+
+# 1. Load AnnData
+adata = ad.read_h5ad("single_cells.h5ad")
+
+# 2. Split into training and test set
+adata_train, adata_test = train_test_split_adata(adata, celltype_col="cell_type", train_frac=0.7)
+
+# 3. Create reference profiles and hierarchy (single layer example)
+X_sub = create_reference(adata_train, celltype_col="cell_type")
+A_l = [pd.DataFrame(np.eye(X_sub.shape[1]), index=X_sub.columns, columns=X_sub.columns)]
+X_l = [X_sub]
+
+# 4. Simulate training bulks
+Y_train, C_train = create_bulks(adata_train, n_bulks=1000, n_cells_per_bulk=100, celltype_col="cell_type")
+
+# 5. Simulate test bulks
+Y_test, C_test = create_bulks(adata_test, n_bulks=100, n_cells_per_bulk=100, celltype_col="cell_type")
+
+# 6. Initialize and train model
+hide = HIDE(X_l, A_l)
+hide.train(Y_train, C_train, iter=1000)
+
+# 7. Deconvolution on test data
+results = hide.predict(Y_test, norm=True)["prediction"]
+
+# 8. Optional: Difference in composition analysis
+# (requires a sample sheet with columns 'SampleID' and 'Cohort')
+
+# sample_sheet = read_csv("sample_sheet.csv")
+# diff = run_mann_whitney_u(results[0], sample_sheet, sample_id_col="SampleID", cohort_col="Cohort")
+```
+
+---
+
+## Citation
+HIDE-deconv's deconvolution algorithm is based on HIDE: Hierarchical Cell Type Deconvolution. If you use HIDE-deconv, please cite the following article.
+
+Dennis Völkl, Malte Mensching-Buhr, Thomas Sterr, Sarah Bolz, Andreas Schäfer, Nicole Seifert, Jana Tauschke, Austin Rayford, Oddbjørn Straume, Helena U Zacharias, Sushma Nagaraja Grellscheid, Tim Beissbarth, Michael Altenbuchinger, Franziska Görtler, HIDE: hierarchical cell-type deconvolution, Bioinformatics, Volume 41, Issue Supplement_1, July 2025, Pages i207–i216, https://doi.org/10.1093/bioinformatics/btaf179
+
+---
+
+## License
+
+This project is licensed under the MIT License.
+
+---
+
+## Contact
+
+For questions, support or scientific collaboration:
+- Dennis Voelkl: dennis.k.voelkl(at)uib.no
+- Franziska Goertler: Franziska.Gortler(at)uib.no
+
+---

hide_deconv-0.1.0/pyproject.toml

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+[project]
+name = "hide-deconv"
+version = "0.1.0"
+description = "HIDE-Deconv - Hierarchical Cell Type Deconvolution"
+authors = [
+    {name = "Dennis Voelkl",email = "dennis.k.volkl@uib.no"},
+    {name = "Franziska Goertler",email = "Franziska.Gortler@uib.no"}
+]
+license = "MIT"
+readme = "README.md"
+requires-python = ">=3.12,<3.15"
+dependencies = [
+    "anndata (>=0.12.10,<0.13.0)",
+    "torch (>=2.11.0,<3.0.0)",
+    "cvxpy (>=1.8.2,<2.0.0)",
+    "gurobipy (>=13.0.1,<14.0.0)",
+    "numpy (>=2.4.4,<3.0.0)",
+    "pandas (>=2.3.3,<3.0.0)",
+    "click (>=8.3.2,<9.0.0)",
+    "scikit-learn (>=1.8.0,<2.0.0)",
+    "scipy (>=1.17.1,<2.0.0)",
+    "inquirerpy (>=0.3.4,<0.4.0)",
+    "rich (>=14.3.3,<15.0.0)",
+    "seaborn (>=0.13.2,<0.14.0)",
+    "scikit-posthocs (>=0.12.0,<0.13.0)",
+    "requests (>=2.33.1,<3.0.0)",
+    "scanpy (>=1.12.1,<2.0.0)",
+    "lifelines (>=0.30.3,<0.31.0)"
+]
+
+[project.urls]
+Homepage = "https://github.com/dvoelkl/HIDE-deconv"
+Repository = "https://github.com/dvoelkl/HIDE-deconv"
+Issues = "https://github.com/dvoelkl/HIDE-deconv/issues"
+
+
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[project.scripts]
+hide-deconv = "hide_deconv.cli:cli"
+[dependency-groups]
+dev = [
+    "pytest (>=9.0.3,<10.0.0)"
+]