cellsweep 0.1.0__tar.gz

cellsweep-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: cellsweep
+Version: 0.1.0
+Summary: Denoising scRNA-seq in a smart and efficient way.
+Author-email: Maya Caskey <mcaskey@caltech.edu>, Joseph Rich <jmrich@caltech.edu>
+Maintainer-email: Maya Caskey <mcaskey@caltech.edu>, Joseph Rich <jmrich@caltech.edu>
+Project-URL: Homepage, https://github.com/pachterlab/cellsweep
+Keywords: bioinformatics,machine learning,single-cell,scRNA-seq,denoising,data-analysis
+Classifier: Environment :: Console
+Classifier: Framework :: Jupyter
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Utilities
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: numba>=0.56.2
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: anndata
+Requires-Dist: pydantic<3.0,>=2.5
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: black[jupyter]>=22.0.0; extra == "dev"
+Requires-Dist: isort>=6.0.0; extra == "dev"
+Requires-Dist: pympler>=1.1; extra == "dev"
+Provides-Extra: analysis
+Requires-Dist: nbval>=0.10.0; extra == "analysis"
+Requires-Dist: nbdime>=4.0.2; extra == "analysis"
+Requires-Dist: ipython>=8.0.0; extra == "analysis"
+Requires-Dist: upsetplot; extra == "analysis"
+Requires-Dist: PyYAML; extra == "analysis"
+Requires-Dist: scanpy; extra == "analysis"
+Requires-Dist: seaborn; extra == "analysis"
+Requires-Dist: matplotlib; extra == "analysis"
+Requires-Dist: celltypist; extra == "analysis"
+Requires-Dist: mpl-scatter-density; extra == "analysis"
+Requires-Dist: astropy; extra == "analysis"
+Requires-Dist: scikit-learn; extra == "analysis"
+Requires-Dist: ipywidgets; extra == "analysis"
+Requires-Dist: torch; extra == "analysis"
+Requires-Dist: scikit-misc; extra == "analysis"
+Requires-Dist: adjustText; extra == "analysis"
+Requires-Dist: squidpy; extra == "analysis"
+Requires-Dist: tqdm; extra == "analysis"
+
+# cellsweep
+
+Sweep out noisy counts from single-cell RNA-seq data with CellSweep!
+
+![alt text](https://github.com/pachterlab/cellsweep/blob/main/figures/logo.png?raw=true)
+
+## Install
+### Basic use
+```
+pip install cellsweep
+```
+
+### To run notebooks:
+```
+pip install cellsweep[analysis]
+```
+
+### To remake figures from the paper:
+```
+git clone https://github.com/pachterlab/cellsweep.git
+cd cellsweep
+conda env create -f environment.yml
+pip install cellsweep[analysis]==0.1.0
+```
+
+## Quickstart
+CellSweep has a single function denoise_count_matrix that takes a raw count matrix in an AnnData object and produces a denoised count matrix in another AnnData object. See a simple, fully worked example in the `notebooks/intro.ipynb` Jupyter Notebook.
+
+### Python API
+```python
+import cellsweep
+adata_cellsweep = cellsweep.denoise_count_matrix(adata_raw_path, adata_out=adata_cellsweep_path)  # assumes that adata_raw_path is an h5ad file or AnnData object with a column adata.obs['celltype'] indicating celltype
+
+# for help
+help(cellsweep.denoise_count_matrix)
+```
+
+### Command line interface
+```
+cellsweep denoise_count_matrix -o adata_cellsweep.h5ad adata_raw.h5ad  # assumes that adata_raw.h5ad is an h5ad file with a column adata.obs['celltype'] indicating celltype
+
+# for help
+cellsweep denoise_count_matrix --help
+```
+
+There are many utility functions in the `cellsweep.utils` module for data processing, plotting, and analysis. See examples in our Jupyter Notebooks.
+
+## Tutorials
+We have several Jupyter Notebooks demonstrating the use of CellSweep for denoising count matrices and analyzing the results. See the `notebooks` folder in the repository.

cellsweep-0.1.0/README.md

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+# cellsweep
+
+Sweep out noisy counts from single-cell RNA-seq data with CellSweep!
+
+![alt text](https://github.com/pachterlab/cellsweep/blob/main/figures/logo.png?raw=true)
+
+## Install
+### Basic use
+```
+pip install cellsweep
+```
+
+### To run notebooks:
+```
+pip install cellsweep[analysis]
+```
+
+### To remake figures from the paper:
+```
+git clone https://github.com/pachterlab/cellsweep.git
+cd cellsweep
+conda env create -f environment.yml
+pip install cellsweep[analysis]==0.1.0
+```
+
+## Quickstart
+CellSweep has a single function denoise_count_matrix that takes a raw count matrix in an AnnData object and produces a denoised count matrix in another AnnData object. See a simple, fully worked example in the `notebooks/intro.ipynb` Jupyter Notebook.
+
+### Python API
+```python
+import cellsweep
+adata_cellsweep = cellsweep.denoise_count_matrix(adata_raw_path, adata_out=adata_cellsweep_path)  # assumes that adata_raw_path is an h5ad file or AnnData object with a column adata.obs['celltype'] indicating celltype
+
+# for help
+help(cellsweep.denoise_count_matrix)
+```
+
+### Command line interface
+```
+cellsweep denoise_count_matrix -o adata_cellsweep.h5ad adata_raw.h5ad  # assumes that adata_raw.h5ad is an h5ad file with a column adata.obs['celltype'] indicating celltype
+
+# for help
+cellsweep denoise_count_matrix --help
+```
+
+There are many utility functions in the `cellsweep.utils` module for data processing, plotting, and analysis. See examples in our Jupyter Notebooks.
+
+## Tutorials
+We have several Jupyter Notebooks demonstrating the use of CellSweep for denoising count matrices and analyzing the results. See the `notebooks` folder in the repository.

cellsweep-0.1.0/cellsweep/__init__.py

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+"""cellsweep package initialization module."""
+
+from .model import denoise_count_matrix
+# from .utils import *  # only imports what is in __all__ in .utils/__init__.py
+
+__version__ = "0.1.0"
+__author__ = "Joseph Rich"
+__email__ = "josephrich98@gmail.com"

cellsweep-0.1.0/cellsweep/constants.py

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+"""cellsweep constant values."""
+
+CellBender_Fig2_to_Immune_All_High_celltype_mapping = {
+    "Monocytes/neutrophils": [
+        "Monocytes", "Mono-mac", "Monocyte precursor", "Macrophages", "Granulocytes"
+    ],
+
+    "Monocytes/pDCs": [
+        "DC", "DC precursor", "pDC", "pDC precursor", "MNP"
+    ],
+
+    "T": [
+        "T cells", "Double-negative thymocytes", "Double-positive thymocytes", "ETP"
+    ],
+
+    "B": [
+        "B cells", "B-cell lineage", "Plasma cells"
+    ],
+
+    "NK": [
+        "ILC", "ILC precursor"  # ILCs include NK-like subsets
+    ],
+
+    "Progenitor": [
+        "HSC/MPP", "Early MK", "Megakaryocyte precursor"
+    ],
+
+    "Baso./neutro./progenitor": [
+        "Promyelocytes", "Myelocytes"
+    ],
+
+}
+
+
+# Broad-to-fine mapping
+CellBender_Fig2_to_Immune_All_Low_celltype_mapping = {
+    "Monocytes/neutrophils": [
+        "Classical monocytes", "Non-classical monocytes", "Monocytes",
+        "Intermediate macrophages", "Intestinal macrophages", "Macrophages",
+        "Kupffer cells", "Kidney-resident macrophages", "Erythrophagocytic macrophages",
+        "Neutrophils", "Granulocytes", "Mono-mac", "Monocyte precursor"
+    ],
+
+    "Monocytes/pDCs": [
+        "pDC", "pDC precursor", "DC", "DC1", "DC2", "DC3",
+        "Transitional DC", "Migratory DCs", "Cycling DCs", "DC precursor"
+    ],
+
+    "TrueT CD4+ naive/Treg": [
+        "Tcm/Naive helper T cells", "Type 1 helper T cells", "Type 17 helper T cells",
+        "Regulatory T cells", "Treg(diff)", "Follicular helper T cells"
+    ],
+
+    "B": [
+        "B cells", "Cycling B cells", "Transitional B cells", "Age-associated B cells"
+    ],
+
+    "B naive": [
+        "Naive B cells", "Pre-pro-B cells", "Pro-B cells", "Small pre-B cells", "Large pre-B cells"
+    ],
+
+    "B memory": [
+        "Memory B cells", "Germinal center B cells", "Proliferative germinal center B cells"
+    ],
+
+    "T CD8+": [
+        "CD8a/a", "CD8a/b(entry)"
+    ],
+
+    "T cytotoxic": [
+        "Tem/Temra cytotoxic T cells", "Tem/Trm cytotoxic T cells",
+        "Trm cytotoxic T cells", "Tcm/Naive cytotoxic T cells",
+        "Memory CD4+ cytotoxic T cells"
+    ],
+
+    "T gd": [
+        "gamma-delta T cells", "CRTAM+ gamma-delta T cells", "Cycling gamma-delta T cells"
+    ],
+
+    "MAIT": [
+        "MAIT cells"
+    ],
+
+    "NK": [
+        "NK cells", "CD16+ NK cells", "CD16- NK cells",
+        "Cycling NK cells", "Transitional NK"
+    ],
+
+    "Monocyte NC/I": [
+        "Non-classical monocytes", "Intermediate macrophages"
+    ],
+
+    "Progenitor": [
+        "HSC/MPP", "CMP", "GMP", "MEMP", "ELP", "ETP",
+        "Early lymphoid/T lymphoid", "Early MK", "Megakaryocyte precursor",
+        "Megakaryocyte-erythroid-mast cell progenitor"
+    ],
+
+    "Baso./neutro./progenitor": [
+        "Promyelocytes", "Myelocytes", "Neutrophil-myeloid progenitor"
+    ],
+
+    "pDCs": [
+        "pDC", "pDC precursor"
+    ]
+}
+
+
+CellTypistHigh_to_ImmuneMajor = {
+    "Monocytes": "Monocytes",
+    "Mono-mac": "Monocytes",
+    "Monocyte precursor": "Macrophages",
+    "Macrophages": "Macrophages",
+    "Granulocytes": "Neutrophils",
+    "DC": "DC",
+    "DC precursor": "DC",
+    "pDC": "DC",
+    "pDC precursor": "DC",
+    "MNP": "Neutrophils",
+    "B cells": "B cells",
+    "B-cell lineage": "B cells",
+    "Plasma cells": "B cells",
+    "T cells": "CD4 T cells",
+    "Double-negative thymocytes": "CD4 T cells",
+    "Double-positive thymocytes": "CD4 T cells",
+    "ETP": "CD4 T cells",
+}
+
+CellTypistLow_to_ImmuneMajor = {
+
+    # ---- Monocytes/neutrophils ----
+    "Classical monocytes": "Monocytes",
+    "Non-classical monocytes": "Monocytes",
+    "Monocytes": "Monocytes",
+    "Monocyte precursor": "Monocytes",
+    "Mono-mac": "Monocytes",
+    
+    "Intermediate macrophages": "Macrophages",
+    "Intestinal macrophages": "Macrophages",
+    "Macrophages": "Macrophages",
+    "Kupffer cells": "Macrophages",
+    "Kidney-resident macrophages": "Macrophages",
+    "Erythrophagocytic macrophages": "Macrophages",
+
+    "Neutrophils": "Neutrophils",
+    "Granulocytes": "Neutrophils",
+
+    # ---- Monocytes/pDCs ----
+    "pDC": "DC",
+    "pDC precursor": "DC",
+    "DC": "DC",
+    "DC1": "DC",
+    "DC2": "DC",
+    "DC3": "DC",
+    "Transitional DC": "DC",
+    "Migratory DCs": "DC",
+    "Cycling DCs": "DC",
+    "DC precursor": "DC",
+
+    # ---- CD4 T ----
+    "Tcm/Naive helper T cells": "CD4 T cells",
+    "Type 1 helper T cells": "CD4 T cells",
+    "Type 17 helper T cells": "CD4 T cells",
+    "Regulatory T cells": "CD4 T cells",
+    "Treg(diff)": "CD4 T cells",
+    "Follicular helper T cells": "CD4 T cells",
+
+    # ---- B ----
+    "B cells": "B cells",
+    "Cycling B cells": "B cells",
+    "Transitional B cells": "B cells",
+    "Age-associated B cells": "B cells",
+    "Naive B cells": "B cells",
+    "Pre-pro-B cells": "B cells",
+    "Pro-B cells": "B cells",
+    "Small pre-B cells": "B cells",
+    "Large pre-B cells": "B cells",
+    "Memory B cells": "B cells",
+    "Germinal center B cells": "B cells",
+    "Proliferative germinal center B cells": "B cells",
+
+    # ---- CD8 ----
+    "CD8a/a": "CD8 T cells",
+    "CD8a/b(entry)": "CD8 T cells",
+    "Tem/Temra cytotoxic T cells": "CD8 T cells",
+    "Tem/Trm cytotoxic T cells": "CD8 T cells",
+    "Trm cytotoxic T cells": "CD8 T cells",
+    "Tcm/Naive cytotoxic T cells": "CD8 T cells",
+    "Memory CD4+ cytotoxic T cells": "CD8 T cells",
+    "gamma-delta T cells": "CD8 T cells",
+    "CRTAM+ gamma-delta T cells": "CD8 T cells",
+    "Cycling gamma-delta T cells": "CD8 T cells",
+    "MAIT cells": "CD8 T cells",
+
+    # ---- NK ----
+    "NK cells": "NK cells",
+    "CD16+ NK cells": "NK cells",
+    "CD16- NK cells": "NK cells",
+    "Cycling NK cells": "NK cells",
+    "Transitional NK": "NK cells",
+
+    # ---- Progenitor ----
+    "HSC/MPP": "Monocytes",   # default major category for HSC/MPP if forced into one bucket
+    "CMP": "Monocytes",
+    "GMP": "Neutrophils",
+    "MEMP": "Eosinophils",
+    "ELP": "B cells",
+    "ETP": "CD4 T cells",
+    "Early lymphoid/T lymphoid": "CD4 T cells",
+    "Early MK": "Monocytes",
+    "Megakaryocyte precursor": "Monocytes",
+    "Megakaryocyte-erythroid-mast cell progenitor": "Eosinophils",
+
+    # ---- Baso/neutro/progenitor ----
+    "Promyelocytes": "Neutrophils",
+    "Myelocytes": "Neutrophils",
+    "Neutrophil-myeloid progenitor": "Neutrophils",
+}
+
+immune_markers = {
+    "Monocytes": ["CD14", "LYZ", "FCGR3A", "MS4A7"],
+    "Macrophages": ["CD68", "CD163", "C1QA", "C1QB", "C1QC"],
+    "DC": ["CLEC9A", "XCR1", "CD1C", "FCER1A", "IL3RA", "TCF4", "ITGAX", "CST3"],
+    "Neutrophils": ["S100A8", "S100A9", "MPO", "FCGR3B", "ELANE"],
+    "Eosinophils": ["CLC", "RNASE2", "RNASE3", "PRG2"],
+    "CD8 T cells": ["CD8A", "CD8B", "GZMB", "CD3E"],
+    "CD4 T cells": ["CD4", "CCR7", "IL7R", "TCF7", "CD3E"],
+    "NK cells": ["NKG7", "GNLY", "PRF1", "KLRD1", "GZMB"],
+    "B cells": ["MS4A1", "CD79A", "CD79B", "HLA-DRA", "CD19"]
+}

cellsweep-0.1.0/cellsweep/main.py

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+"""main function for argparse."""
+
+import argparse
+import sys
+from .__init__ import __version__
+from .model import denoise_count_matrix
+
+# Custom formatter for help messages that preserved the text formatting and adds the default value to the end of the help message
+class CustomHelpFormatter(argparse.RawTextHelpFormatter):
+    def _get_help_string(self, action):
+        help_str = action.help if action.help else ""
+        if (
+            "%(default)" not in help_str
+            and action.default is not argparse.SUPPRESS
+            and action.default is not None
+            # default information can be deceptive or confusing for boolean flags.
+            # For example, `--quiet` says "Does not print progress information. (default: True)" even though
+            # the default action is to NOT be quiet (to the user, the default is False).
+            and not isinstance(action, argparse._StoreTrueAction)
+            and not isinstance(action, argparse._StoreFalseAction)
+        ):
+            help_str += " (default: %(default)s)"
+        return help_str
+
+
+def main():  # noqa: C901
+    """
+    Function containing argparse parsers and arguments to allow the use of cellsweep from the terminal (as cellsweep).
+    """
+
+    parent_parser = argparse.ArgumentParser(description=f"cellsweep v{__version__}", add_help=False)  # Define parent parser
+    parent_subparsers = parent_parser.add_subparsers(dest="command")  # Initiate subparsers
+    parent = argparse.ArgumentParser(add_help=False)
+
+    # Add custom help argument to parent parser
+    parent_parser.add_argument("-h", "--help", action="store_true", help="Print manual.")
+    # Add custom version argument to parent parser
+    parent_parser.add_argument("-v", "--version", action="store_true", help="Print version.")
+
+    denoise_count_matrix_desc = "Denoise count matrix using cellsweep."
+
+    parser_denoise_count_matrix = parent_subparsers.add_parser(
+        "denoise_count_matrix",
+        parents=[parent],
+        description=denoise_count_matrix_desc,
+        help=denoise_count_matrix_desc,
+        add_help=True,
+        formatter_class=CustomHelpFormatter,
+    )
+
+    parser_denoise_count_matrix.add_argument(
+        "adata",
+        type=str,
+        help="Path to input AnnData file (.h5ad) containing raw count matrix in .X.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "-o",
+        "--adata_out",
+        type=str,
+        default="adata_denoised.h5ad",
+        help="Path to output AnnData file (.h5ad) to save denoised count matrix.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--max_iter",
+        type=int,
+        default=2000,
+        help="Maximum number of EM iterations.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--init_alpha",
+        type=float,
+        default=0.9,
+        help="Initial value of alpha_n for each cell.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--alpha_cap",
+        type=float,
+        default=0.9,
+        help="alpha_n is not allowed to surpass this value in the first stage of training (before ll convergence). Barcodes that attempt to pass this threshold will be excluded from updating p_k and allowed to change cell-types.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--init_beta",
+        type=float,
+        default=0.1,
+        help="Initial beta (percent bulk contamination) value for each cell.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--eps",
+        type=float,
+        default=1e-12,
+        help="Numerical stability constant to prevent division by zero).",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--log_eps",
+        type=float,
+        default=1e-300,
+        help="Numerical stability constant to prevent log(0).",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--celltype_lambda",
+        type=float,
+        default=10,
+        help="Pseudocount for celltype profile update. Higher values lead to smoother celltype profiles",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--ambient_lambda",
+        type=float,
+        default=50,
+        help="Pseudocount for ambient profile update. Higher values lead to a smoother ambient profile.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--bulk_lambda",
+        type=float,
+        default=10,
+        help="Pseudocount for bulk profile update. Higher values lead to a smoother bulk profile.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--repulsion_strength",
+        type=float,
+        default=1e-4,
+        help="Strength of repulsion between ambient and cell-type profiles during M-step. Higher values lead to greater separation between ambient and cell-type profiles.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--max_frac_gene_repulsion",
+        type=float,
+        default=0.2,
+        help="Maximum fraction of each p_k entry that can be subtracted during repulsion.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--round_X",
+        action="store_true",
+        help="If True, rounds denoised counts to nearest integer before saving.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "-t", "--threads",
+        type=int,
+        default=1,
+        help="number of numba threads",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--disable_freeze_empty",
+        action="store_false",
+        help="If True, does not attempt to reestimate empty droplets."
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--disable_freeze_ambient_profile",
+        action="store_false",
+        help="If True, does not update the ambient profile (a) based on alpha."
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--empty_droplet_method",
+        type=str,
+        default="threshold",
+        choices=["threshold"],
+        help="Strategy to infer empty droplets if `is_empty` is not present."
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--umi_cutoff",
+        type=int,
+        default=None,
+        help="Optional absolute UMI count threshold for classifying droplets as empty."
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--expected_cells",
+        type=int,
+        default=None,
+        help="Expected number of real cells, used when estimating thresholds."
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--del0_ll_tol",
+        type=float,
+        default=1e-3,
+        help="The change in likelihood, relative to the first likelihood step, below which repulsion and cell-type reassignment are discontinued and convergence is checked."
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--min_ll_tol",
+        type=float,
+        default=1e-6,
+        help="The change in likelihood, relative to the current likelihood step, below which repulsion and cell-type reassignment are discontinued and convergence is checked. This is intended to cap `del0_ll_tol` at the edge of floating-point precision."
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--tol_p",
+        type=float,
+        default=1e-4,
+        help="The maximum change in p below which training is discontinued. This is in addition to the tol_f stopping criterion.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--tol_f",
+        type=float,
+        default=1e-4,
+        help="The maximum change in f = (1 - beta) * alpha + beta, below which training is discontinued. This is in addition to the tol_p stopping criterion.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--random_state",
+        type=int,
+        default=42,
+        help="Random seed.",
+    )
+    parser_denoise_count_matrix.add_argument(
+        "-v", "--verbose",
+        action="count",
+        default=0,
+        help="Verbosity level. Default logging.WARNING, -v logging.INFO, -vv for logging.DEBUG)"
+    )
+    parser_denoise_count_matrix.add_argument(
+        "--quiet",
+        action="store_true",
+        help="Suppress all output (overrides any verbose flag)",
+    )
+    # no need because adata is always a file path in CLI
+    # parser_denoise_count_matrix.add_argument(
+    #     "--disable_copy_anndata",
+    #     action="store_false",
+    #     help="If adata is an Anndata object, then copy it to avoid modifying the input in-place."
+    # )
+    parser_denoise_count_matrix.add_argument(
+        "--log_file",
+        type=str,
+        default=None,
+        help="Optional path to save EM iteration logs.",
+    )
+
+    args, unknown_args = parent_parser.parse_known_args()
+
+    # Help return
+    if args.help:
+        # Retrieve all subparsers from the parent parser
+        subparsers_actions = [action for action in parent_parser._actions if isinstance(action, argparse._SubParsersAction)]
+        for subparsers_action in subparsers_actions:
+            # Get all subparsers and print help
+            for choice, subparser in subparsers_action.choices.items():
+                print("Subparser '{}'".format(choice))
+                print(subparser.format_help())
+        sys.exit(1)
+
+    # Version return
+    if args.version:
+        print(f"varseek version: {__version__}")
+        sys.exit(1)
+
+    # Show help when no arguments are given
+    if len(sys.argv) == 1:
+        parent_parser.print_help(sys.stderr)
+        sys.exit(1)
+    
+    command_to_parser = {
+        "denoise_count_matrix": parser_denoise_count_matrix,
+    }
+    
+    if len(sys.argv) == 2:
+        if sys.argv[1] in command_to_parser:
+            command_to_parser[sys.argv[1]].print_help(sys.stderr)
+        else:
+            parent_parser.print_help(sys.stderr)
+        sys.exit(1)
+    
+    if args.command == "denoise_count_matrix":
+        denoise_count_matrix(
+            adata=args.adata,
+            adata_out=args.adata_out,
+            max_iter=args.max_iter,
+            init_alpha=args.init_alpha,
+            alpha_cap=args.alpha_cap,
+            beta=args.int_beta,
+            eps=args.eps,
+            log_eps=args.log_eps,
+            celltype_lambda=args.celltype_lambda,
+            ambient_lambda=args.ambient_lambda,
+            bulk_lambda=args.bulk_lambda,
+            repulsion_strength=args.repulsion_strength,
+            max_frac_gene_repulsion=args.max_frac_gene_repulsion,
+            round_X=args.round_X,
+            threads=args.threads,
+            freeze_empty=args.disable_freeze_empty,
+            empty_droplet_method=args.empty_droplet_method,
+            umi_cutoff=args.umi_cutoff,
+            expected_cells=args.expected_cells,
+            tol=args.tol,
+            min_tol=args.min_tol,
+            tol_p=args.tol_p,
+            tol_f=args.tol_f,
+            random_state=args.random_state,
+            verbose=args.verbose,
+            quiet=args.quiet,
+            log_file=args.log_file,
+        )
+