multineuronchat 2025.11.10.dev0__py3-none-any.whl

multineuronchat-2025.11.10.dev0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: multineuronchat
+Version: 2025.11.10.dev0
+Summary: MultiNeuronChat is a Python library for inferring condition‑related changes in synaptic cell‑cell communication from scRNA-/snRNA-Seq datasets in case vs control study designs.
+Author-email: Gianluca Volkmer <gianluca.volkmer@ki.se>
+License-Expression: GPL-3.0
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy==1.26.4
+Requires-Dist: pandas==2.3.1
+Requires-Dist: xarray==2025.7.1
+Requires-Dist: dask==2025.7.0
+Requires-Dist: netCDF4==1.7.2
+Requires-Dist: bottleneck==1.5.0
+Requires-Dist: scipy==1.16.1
+Requires-Dist: matplotlib==3.10.5
+Requires-Dist: seaborn==0.13.2
+Requires-Dist: tqdm==4.67.1
+Requires-Dist: loompy==3.0.8
+Dynamic: license-file
+
+# MultiNeuronChat
+
+**MultiNeuronChat** is a Python library for inferring *condition‑related changes* in synaptic cell‑cell communication from single‑cell / single‑nucleus RNA‑seq (sc/snRNA‑seq) datasets in **case vs control** study designs.  
+It builds on the mathematical model of [Zhao _et al._ 2023](https://www.nature.com/articles/s41467-023-36800-w) method [NeuronChat](https://github.com/Wei-BioMath/NeuronChat) and extends it to multi‑condition comparisons with subject‑level statistics.
+
+---
+## Installation
+
+From PyPI:
+
+```bash
+pip install multineuronchat
+```
+
+> Python ≥ 3.9 is recommended.
+---
+
+## Quick start (minimal end-to-end)
+
+MultiNeuronChat expects a **cell-wise log-normalized** gene expression matrix in [**Loom**](https://linnarssonlab.org/loompy/) format. You can either normalize your matrix manually or use the provided implementation:
+
+```python
+from multineuronchat.normalize import cell_wise_log_normalization
+
+cell_wise_log_normalization(
+    # Path to the input Loom file 
+    path_to_loom="path/to/data.loom",
+    # Path to the cell-wise log-normalized output Loom file
+    path_to_normalized_loom='path/to/cellwise_normalized_data.loom',
+    # Whether to print computational progress
+    verbose=True
+)
+```
+
+This log-normalized loom file can then be used to run MultiNeuronChat:
+
+```python
+from multineuronchat.MultiNeuronChatObject import MultiNeuronChatObject
+
+# 1) Configure your analysis
+mnc = MultiNeuronChatObject(
+    condition_label_column="condition",           # column attribute in Loom
+    condition_names=("control", "case"),          # order matters
+    subject_label_column="subject",               # column attribute in Loom
+    cell_type_label_column="cell_types",          # column attribute in Loom
+    db="human_extended"                           # "human", "mouse", "human_extended", or path to custom DB
+)
+
+# 2) Compute communication scores
+mnc.compute_communication_scores(
+    # Path to the cell-wise log-normalized Loom file
+    path_to_data_loom="path/to/cellwise_normalized_data.loom",
+    # The row name of the gene attribute in the Loom file
+    gene_label_row='gene',
+    # The number of processes to use for the parallel computations of communication scores
+    n_processes=4,
+    # The minimum number of cells of a specific cell type within a specific subject to include in the analysis
+    min_n_cells_threshold=20,
+    # Whether to print computational progress
+    verbose=True
+)
+
+# 3) (Optional) Focus hypotheses with masks (Wasserstein / EMD)
+from multineuronchat.masks import compute_wasserstein_mask
+mask = compute_wasserstein_mask(mnc, top_percentile=99.0)
+
+# 4) Significance testing and multiple testing correction
+pvals = mnc.compute_significance(
+    # The statistical test to use when comparing the communication score distributions between conditions
+    statistical_test='KS',
+    # Optional mask to focus the significance testing on specific interactions. If None, all interactions are tested.
+    mask=mask,
+    # The number of resamples to use for permutation testing when appropriate
+    n_resamples=10_000,
+    # The random state for reproducibility
+    random_state=42
+)
+
+# 5) Control FDR (Benjamini–Yekutieli by default; use "bh" for Benjamini–Hochberg)
+pvals_adj = mnc.correct_p_values(statistical_test="KS", method="by")
+```
+
+
+## Input data requirements
+
+For MultiNeuronChat to function, your input Loom file must meet the following criteria:
+
+- **Row attributes**:
+  - genes that were measured (`gene`)
+- **Column attributes**:
+  - labels assigning a subject to each cell (`subject` in the example above but can be configured)
+  - condition labels (`condition` in the example above but can be configured)
+  - cell type labels (`cell_types` in the example above but can be configured)
+
+> Gene symbols should match the selected interaction database (human, mouse, or your custom DB).

multineuronchat-2025.11.10.dev0.dist-info/RECORD

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multineuronchat-2025.11.10.dev0.dist-info/WHEEL

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+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
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