celljanus 0.1.3__tar.gz

celljanus-0.1.3/LICENSE

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+MIT License
+
+Copyright (c) 2026 Zhaoqing Wang
+
+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.

celljanus-0.1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: celljanus
+Version: 0.1.3
+Summary: CellJanus: Dual-Perspective Deconvolution of Host and Microbial Transcriptomes from FASTQ Data
+Author: Zhaoqing Wang
+License: MIT
+Project-URL: Homepage, https://github.com/zhaoqing-wang/CellJanus
+Project-URL: Repository, https://github.com/zhaoqing-wang/CellJanus
+Project-URL: Changelog, https://github.com/zhaoqing-wang/CellJanus/blob/main/CHANGELOG.md
+Project-URL: Bug Tracker, https://github.com/zhaoqing-wang/CellJanus/issues
+Keywords: bioinformatics,metagenomics,single-cell,spatial-transcriptomics,microbiome,host-microbe,deconvolution,docker
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+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: Programming Language :: Python :: 3.13
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click>=8.1
+Requires-Dist: rich>=13.0
+Requires-Dist: pandas>=2.0
+Requires-Dist: numpy>=1.24
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: seaborn>=0.12
+Requires-Dist: biopython>=1.81
+Requires-Dist: requests>=2.31
+Requires-Dist: tqdm>=4.65
+Requires-Dist: psutil>=5.9
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: black>=23.0; extra == "dev"
+Requires-Dist: ruff>=0.1; extra == "dev"
+Dynamic: license-file
+
+<table>
+  <tr>
+    <td>
+      <h1>CellJanus: Dual-Perspective Deconvolution of Host and Microbial Transcriptomes from FASTQ Data</h1>
+      <p>
+        <a href="https://github.com/zhaoqing-wang/CellJanus/releases"><img src="https://img.shields.io/badge/dynamic/toml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fzhaoqing-wang%2FCellJanus%2Fmain%2Fpyproject.toml&label=Version&query=project.version&color=blue&style=flat-square" alt="Version" /></a>
+        <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-green.svg" alt="License: MIT" /></a>
+        <a href="https://www.python.org/"><img src="https://img.shields.io/badge/Python-3.9%2B-blue.svg" alt="Python 3.9+" /></a>
+        <a href="https://github.com/zhaoqing-wang"><img src="https://img.shields.io/badge/Maintainer-Zhaoqing_Wang-green" alt="GitHub Maintainer" /></a>
+      </p>
+    </td>
+    <td width="200">
+      <img src="docs/Sticker.png" alt="CellJanus Logo" width="200" />
+    </td>
+  </tr>
+</table>
+
+## Pipeline
+
+```
+FASTQ ─→ fastp (QC) ─→ Bowtie2 (host alignment) ─→ unmapped reads
+                             │                            │
+                             ▼                            ▼
+                    host_aligned.bam           Kraken2 + Bracken  ─→  plots (PNG/PDF) + CSV tables
+                   (gene expression)        (microbial abundance)
+```
+
+## Contents
+
+1. [Installation](#installation)
+2. [Quick Start](#quick-start)
+3. [Real Data](#real-data)
+4. [CLI Reference](#cli-reference)
+5. [Python API](#python-api)
+6. [Output Structure](#output-structure)
+7. [Citation](#citation)
+
+---
+
+## Installation
+
+> Requires **Linux / macOS / WSL2**. Bioconda packages are not available on native Windows.
+
+```bash
+# Create conda environment with all dependencies
+conda create -n CellJanus -c bioconda -c conda-forge \
+    python=3.11 fastp bowtie2 samtools kraken2 bracken
+
+# Install CellJanus
+conda activate CellJanus
+git clone https://github.com/zhaoqing-wang/CellJanus.git
+cd CellJanus
+pip install .
+
+# Verify installation
+celljanus check
+```
+
+All tools should show **✔ Found**. STAR is optional (for future RNA-seq alignment support).
+
+<details>
+<summary>Docker alternative</summary>
+
+```bash
+docker build -t celljanus .
+docker run --rm celljanus celljanus check
+```
+</details>
+
+---
+
+## Quick Start
+
+The repository includes test data and pre-built reference databases — run the full pipeline immediately with **no downloads required**.
+
+```bash
+conda activate CellJanus
+cd CellJanus
+
+celljanus run \
+    --read1 testdata/reads_R1.fastq.gz \
+    --read2 testdata/reads_R2.fastq.gz \
+    --host-index testdata/refs/host_genome/host \
+    --kraken2-db testdata/refs/kraken2_testdb \
+    --output-dir test_results \
+    --threads 4
+```
+
+**Test data**: 1,000 paired-end reads (600 human, 300 microbial, 100 low-quality).
+
+**Results** (~4 seconds):
+
+| Step | Metric |
+|------|--------|
+| QC | 1,000 → 900 pairs retained (90%), Q20 improved 88% → 98% |
+| Host alignment | 66.39% aligned to host genome |
+| Classification | 300 reads classified → 3 species detected |
+| Top species | *S. aureus* 38.7%, *K. pneumoniae* 31.3%, *E. coli* 30.0% |
+| Output | 8 plots (PNG + PDF), 3 CSV tables, QC reports |
+
+#### Example Output
+
+| Pipeline Dashboard |
+|:--:|
+| ![Pipeline Dashboard](docs/pipeline_dashboard.png) |
+| *Summarises QC, alignment and classification metrics in a single view.* |
+
+| Abundance Bar Chart | Abundance Donut Chart | Abundance Heatmap |
+|:--:|:--:|:--:|
+| ![Bar](docs/abundance_bar.png) | ![Pie](docs/abundance_pie.png) | ![Heatmap](docs/abundance_heatmap.png) |
+| Top species ranked by read count. | Relative proportion of each species. | Log₁₀-scaled heatmap of species abundance. |
+
+### Run Individual Steps
+
+```bash
+# QC only
+celljanus qc -1 testdata/reads_R1.fastq.gz -2 testdata/reads_R2.fastq.gz -o results/01_qc
+
+# Align to host
+celljanus align -1 results/01_qc/reads_R1_qc.fastq.gz \
+    -2 results/01_qc/reads_R2_qc.fastq.gz \
+    -x testdata/refs/host_genome/host -o results/02_alignment
+
+# Classify microbial reads
+celljanus classify -1 results/02_alignment/unmapped_R1.fastq.gz \
+    -2 results/02_alignment/unmapped_R2.fastq.gz \
+    -d testdata/refs/kraken2_testdb -o results/04_classification
+
+# Generate plots
+celljanus visualize -b results/04_classification/bracken_S.txt -o results/05_visualisation
+```
+
+---
+
+## Real Data
+
+### 1. Download reference databases
+
+```bash
+# Human genome hg38 + Bowtie2 index (~5 GB)
+celljanus download hg38 -o ./refs
+
+# Kraken2 standard database (~8 GB)
+celljanus download kraken2 -o ./refs --db-name standard_8
+```
+
+### 2. Run pipeline
+
+```bash
+celljanus run \
+    -1 /path/to/sample_R1.fastq.gz \
+    -2 /path/to/sample_R2.fastq.gz \
+    -x ./refs/bowtie2_index/GRCh38_noalt_as \
+    -d ./refs/standard_8 \
+    -o ./results \
+    --threads 8
+```
+
+### Key Options
+
+| Option | Default | Description |
+|--------|---------|-------------|
+| `-1, --read1` | *required* | R1 FASTQ (or single-end FASTQ) |
+| `-2, --read2` | — | R2 FASTQ for paired-end |
+| `-x, --host-index` | *required* | Bowtie2 index prefix |
+| `-d, --kraken2-db` | *required* | Kraken2 database path |
+| `-o, --output-dir` | `celljanus_output` | Output directory |
+| `-t, --threads` | auto (CPUs − 2) | Worker threads |
+| `--min-quality` | 15 | Phred quality threshold |
+| `--confidence` | 0.05 | Kraken2 confidence |
+| `--bracken-level` | S | Taxonomic level (D/P/C/O/F/G/S) |
+| `--skip-qc` | — | Skip QC step |
+| `--skip-classify` | — | Skip classification |
+| `--skip-visualize` | — | Skip visualisation |
+
+---
+
+## CLI Reference
+
+| Command | Description |
+|---------|-------------|
+| `celljanus run` | Full pipeline: QC → Align → Classify → Visualize |
+| `celljanus qc` | Quality control (fastp) |
+| `celljanus align` | Host alignment + unmapped extraction (Bowtie2) |
+| `celljanus extract` | Extract unmapped reads from BAM |
+| `celljanus classify` | Taxonomic classification (Kraken2 + Bracken) |
+| `celljanus visualize` | Generate abundance plots |
+| `celljanus download` | Download reference databases |
+| `celljanus check` | Verify external tool installation |
+
+Run `celljanus <command> --help` for full option details.
+
+---
+
+## Python API
+
+```python
+from pathlib import Path
+from celljanus.config import CellJanusConfig
+from celljanus.pipeline import run_pipeline
+
+cfg = CellJanusConfig(
+    output_dir=Path("./results"),
+    host_index=Path("./refs/bowtie2_index/GRCh38_noalt_as"),
+    kraken2_db=Path("./refs/standard_8"),
+    threads=8,
+)
+
+result = run_pipeline(
+    Path("sample_R1.fastq.gz"),
+    read2=Path("sample_R2.fastq.gz"),
+    cfg=cfg,
+)
+
+result.bracken_df          # Species abundance (pandas DataFrame)
+result.qc_report.summary() # QC statistics
+```
+
+---
+
+## Output Structure
+
+```
+output_dir/
+├── 01_qc/                           # Quality control
+│   ├── *_qc.fastq.gz               # Trimmed reads
+│   ├── *_fastp.json                 # QC metrics
+│   └── *_fastp.html                 # Interactive report
+├── 02_alignment/                    # Host alignment
+│   ├── host_aligned.sorted.bam      # Full alignment
+│   ├── host_mapped.sorted.bam       # Host-only reads
+│   ├── unmapped_R{1,2}.fastq.gz     # Non-host reads → classification
+│   └── host_align_stats.txt         # Alignment statistics
+├── 04_classification/               # Microbial classification
+│   ├── kraken2_report.txt           # Taxonomic report
+│   ├── kraken2_output.txt           # Per-read assignments
+│   └── bracken_S.txt                # Species abundance
+├── 05_visualisation/plots/          # Figures (PNG + PDF)
+│   ├── abundance_bar.*              # Horizontal bar chart
+│   ├── abundance_pie.*              # Donut chart
+│   ├── abundance_heatmap.*          # Heatmap (log₁₀ scale)
+│   └── pipeline_dashboard.*         # Summary dashboard
+├── 06_tables/                       # Machine-readable results
+│   ├── pipeline_summary.csv         # Per-step metrics
+│   ├── species_abundance.csv        # Species × reads × fraction
+│   └── output_manifest.csv          # File inventory with sizes
+└── celljanus.log                    # Pipeline log
+```
+
+### CSV Tables
+
+**`species_abundance.csv`**:
+
+| name | taxonomy_id | bracken_estimated | fraction_pct |
+|------|-------------|------------------:|--------------:|
+| Staphylococcus aureus | 1280 | 116 | 38.67 |
+| Klebsiella pneumoniae | 573 | 94 | 31.33 |
+| Escherichia coli | 562 | 90 | 30.00 |
+
+**`pipeline_summary.csv`**: one row per metric (Step, Metric, Value) covering QC, alignment, and classification statistics.
+
+---
+
+## Performance
+
+| Component | Memory | Note |
+|-----------|--------|------|
+| fastp | < 1 GB | Streaming I/O |
+| Bowtie2 + hg38 | ~3.5 GB | Memory-mapped index |
+| Kraken2 (standard DB) | ~8 GB | `--memory-mapping` flag |
+| **Peak total** | **~12–14 GB** | Fits a 32 GB laptop |
+
+---
+
+## Citation
+
+```
+Wang Z (2026). CellJanus: A Dual-Perspective Tool for Deconvolving Host
+Single-Cell and Microbial Transcriptomes. Python package version 0.1.3.
+https://github.com/zhaoqing-wang/CellJanus
+```
+
+## License
+
+[MIT](LICENSE)

celljanus-0.1.3/README.md

@@ -0,0 +1,285 @@
+<table>
+  <tr>
+    <td>
+      <h1>CellJanus: Dual-Perspective Deconvolution of Host and Microbial Transcriptomes from FASTQ Data</h1>
+      <p>
+        <a href="https://github.com/zhaoqing-wang/CellJanus/releases"><img src="https://img.shields.io/badge/dynamic/toml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fzhaoqing-wang%2FCellJanus%2Fmain%2Fpyproject.toml&label=Version&query=project.version&color=blue&style=flat-square" alt="Version" /></a>
+        <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-green.svg" alt="License: MIT" /></a>
+        <a href="https://www.python.org/"><img src="https://img.shields.io/badge/Python-3.9%2B-blue.svg" alt="Python 3.9+" /></a>
+        <a href="https://github.com/zhaoqing-wang"><img src="https://img.shields.io/badge/Maintainer-Zhaoqing_Wang-green" alt="GitHub Maintainer" /></a>
+      </p>
+    </td>
+    <td width="200">
+      <img src="docs/Sticker.png" alt="CellJanus Logo" width="200" />
+    </td>
+  </tr>
+</table>
+
+## Pipeline
+
+```
+FASTQ ─→ fastp (QC) ─→ Bowtie2 (host alignment) ─→ unmapped reads
+                             │                            │
+                             ▼                            ▼
+                    host_aligned.bam           Kraken2 + Bracken  ─→  plots (PNG/PDF) + CSV tables
+                   (gene expression)        (microbial abundance)
+```
+
+## Contents
+
+1. [Installation](#installation)
+2. [Quick Start](#quick-start)
+3. [Real Data](#real-data)
+4. [CLI Reference](#cli-reference)
+5. [Python API](#python-api)
+6. [Output Structure](#output-structure)
+7. [Citation](#citation)
+
+---
+
+## Installation
+
+> Requires **Linux / macOS / WSL2**. Bioconda packages are not available on native Windows.
+
+```bash
+# Create conda environment with all dependencies
+conda create -n CellJanus -c bioconda -c conda-forge \
+    python=3.11 fastp bowtie2 samtools kraken2 bracken
+
+# Install CellJanus
+conda activate CellJanus
+git clone https://github.com/zhaoqing-wang/CellJanus.git
+cd CellJanus
+pip install .
+
+# Verify installation
+celljanus check
+```
+
+All tools should show **✔ Found**. STAR is optional (for future RNA-seq alignment support).
+
+<details>
+<summary>Docker alternative</summary>
+
+```bash
+docker build -t celljanus .
+docker run --rm celljanus celljanus check
+```
+</details>
+
+---
+
+## Quick Start
+
+The repository includes test data and pre-built reference databases — run the full pipeline immediately with **no downloads required**.
+
+```bash
+conda activate CellJanus
+cd CellJanus
+
+celljanus run \
+    --read1 testdata/reads_R1.fastq.gz \
+    --read2 testdata/reads_R2.fastq.gz \
+    --host-index testdata/refs/host_genome/host \
+    --kraken2-db testdata/refs/kraken2_testdb \
+    --output-dir test_results \
+    --threads 4
+```
+
+**Test data**: 1,000 paired-end reads (600 human, 300 microbial, 100 low-quality).
+
+**Results** (~4 seconds):
+
+| Step | Metric |
+|------|--------|
+| QC | 1,000 → 900 pairs retained (90%), Q20 improved 88% → 98% |
+| Host alignment | 66.39% aligned to host genome |
+| Classification | 300 reads classified → 3 species detected |
+| Top species | *S. aureus* 38.7%, *K. pneumoniae* 31.3%, *E. coli* 30.0% |
+| Output | 8 plots (PNG + PDF), 3 CSV tables, QC reports |
+
+#### Example Output
+
+| Pipeline Dashboard |
+|:--:|
+| ![Pipeline Dashboard](docs/pipeline_dashboard.png) |
+| *Summarises QC, alignment and classification metrics in a single view.* |
+
+| Abundance Bar Chart | Abundance Donut Chart | Abundance Heatmap |
+|:--:|:--:|:--:|
+| ![Bar](docs/abundance_bar.png) | ![Pie](docs/abundance_pie.png) | ![Heatmap](docs/abundance_heatmap.png) |
+| Top species ranked by read count. | Relative proportion of each species. | Log₁₀-scaled heatmap of species abundance. |
+
+### Run Individual Steps
+
+```bash
+# QC only
+celljanus qc -1 testdata/reads_R1.fastq.gz -2 testdata/reads_R2.fastq.gz -o results/01_qc
+
+# Align to host
+celljanus align -1 results/01_qc/reads_R1_qc.fastq.gz \
+    -2 results/01_qc/reads_R2_qc.fastq.gz \
+    -x testdata/refs/host_genome/host -o results/02_alignment
+
+# Classify microbial reads
+celljanus classify -1 results/02_alignment/unmapped_R1.fastq.gz \
+    -2 results/02_alignment/unmapped_R2.fastq.gz \
+    -d testdata/refs/kraken2_testdb -o results/04_classification
+
+# Generate plots
+celljanus visualize -b results/04_classification/bracken_S.txt -o results/05_visualisation
+```
+
+---
+
+## Real Data
+
+### 1. Download reference databases
+
+```bash
+# Human genome hg38 + Bowtie2 index (~5 GB)
+celljanus download hg38 -o ./refs
+
+# Kraken2 standard database (~8 GB)
+celljanus download kraken2 -o ./refs --db-name standard_8
+```
+
+### 2. Run pipeline
+
+```bash
+celljanus run \
+    -1 /path/to/sample_R1.fastq.gz \
+    -2 /path/to/sample_R2.fastq.gz \
+    -x ./refs/bowtie2_index/GRCh38_noalt_as \
+    -d ./refs/standard_8 \
+    -o ./results \
+    --threads 8
+```
+
+### Key Options
+
+| Option | Default | Description |
+|--------|---------|-------------|
+| `-1, --read1` | *required* | R1 FASTQ (or single-end FASTQ) |
+| `-2, --read2` | — | R2 FASTQ for paired-end |
+| `-x, --host-index` | *required* | Bowtie2 index prefix |
+| `-d, --kraken2-db` | *required* | Kraken2 database path |
+| `-o, --output-dir` | `celljanus_output` | Output directory |
+| `-t, --threads` | auto (CPUs − 2) | Worker threads |
+| `--min-quality` | 15 | Phred quality threshold |
+| `--confidence` | 0.05 | Kraken2 confidence |
+| `--bracken-level` | S | Taxonomic level (D/P/C/O/F/G/S) |
+| `--skip-qc` | — | Skip QC step |
+| `--skip-classify` | — | Skip classification |
+| `--skip-visualize` | — | Skip visualisation |
+
+---
+
+## CLI Reference
+
+| Command | Description |
+|---------|-------------|
+| `celljanus run` | Full pipeline: QC → Align → Classify → Visualize |
+| `celljanus qc` | Quality control (fastp) |
+| `celljanus align` | Host alignment + unmapped extraction (Bowtie2) |
+| `celljanus extract` | Extract unmapped reads from BAM |
+| `celljanus classify` | Taxonomic classification (Kraken2 + Bracken) |
+| `celljanus visualize` | Generate abundance plots |
+| `celljanus download` | Download reference databases |
+| `celljanus check` | Verify external tool installation |
+
+Run `celljanus <command> --help` for full option details.
+
+---
+
+## Python API
+
+```python
+from pathlib import Path
+from celljanus.config import CellJanusConfig
+from celljanus.pipeline import run_pipeline
+
+cfg = CellJanusConfig(
+    output_dir=Path("./results"),
+    host_index=Path("./refs/bowtie2_index/GRCh38_noalt_as"),
+    kraken2_db=Path("./refs/standard_8"),
+    threads=8,
+)
+
+result = run_pipeline(
+    Path("sample_R1.fastq.gz"),
+    read2=Path("sample_R2.fastq.gz"),
+    cfg=cfg,
+)
+
+result.bracken_df          # Species abundance (pandas DataFrame)
+result.qc_report.summary() # QC statistics
+```
+
+---
+
+## Output Structure
+
+```
+output_dir/
+├── 01_qc/                           # Quality control
+│   ├── *_qc.fastq.gz               # Trimmed reads
+│   ├── *_fastp.json                 # QC metrics
+│   └── *_fastp.html                 # Interactive report
+├── 02_alignment/                    # Host alignment
+│   ├── host_aligned.sorted.bam      # Full alignment
+│   ├── host_mapped.sorted.bam       # Host-only reads
+│   ├── unmapped_R{1,2}.fastq.gz     # Non-host reads → classification
+│   └── host_align_stats.txt         # Alignment statistics
+├── 04_classification/               # Microbial classification
+│   ├── kraken2_report.txt           # Taxonomic report
+│   ├── kraken2_output.txt           # Per-read assignments
+│   └── bracken_S.txt                # Species abundance
+├── 05_visualisation/plots/          # Figures (PNG + PDF)
+│   ├── abundance_bar.*              # Horizontal bar chart
+│   ├── abundance_pie.*              # Donut chart
+│   ├── abundance_heatmap.*          # Heatmap (log₁₀ scale)
+│   └── pipeline_dashboard.*         # Summary dashboard
+├── 06_tables/                       # Machine-readable results
+│   ├── pipeline_summary.csv         # Per-step metrics
+│   ├── species_abundance.csv        # Species × reads × fraction
+│   └── output_manifest.csv          # File inventory with sizes
+└── celljanus.log                    # Pipeline log
+```
+
+### CSV Tables
+
+**`species_abundance.csv`**:
+
+| name | taxonomy_id | bracken_estimated | fraction_pct |
+|------|-------------|------------------:|--------------:|
+| Staphylococcus aureus | 1280 | 116 | 38.67 |
+| Klebsiella pneumoniae | 573 | 94 | 31.33 |
+| Escherichia coli | 562 | 90 | 30.00 |
+
+**`pipeline_summary.csv`**: one row per metric (Step, Metric, Value) covering QC, alignment, and classification statistics.
+
+---
+
+## Performance
+
+| Component | Memory | Note |
+|-----------|--------|------|
+| fastp | < 1 GB | Streaming I/O |
+| Bowtie2 + hg38 | ~3.5 GB | Memory-mapped index |
+| Kraken2 (standard DB) | ~8 GB | `--memory-mapping` flag |
+| **Peak total** | **~12–14 GB** | Fits a 32 GB laptop |
+
+---
+
+## Citation
+
+```
+Wang Z (2026). CellJanus: A Dual-Perspective Tool for Deconvolving Host
+Single-Cell and Microbial Transcriptomes. Python package version 0.1.3.
+https://github.com/zhaoqing-wang/CellJanus
+```
+
+## License
+
+[MIT](LICENSE)

celljanus-0.1.3/celljanus/__init__.py

@@ -0,0 +1,10 @@
+"""
+CellJanus: A Dual-Perspective Tool for Deconvolving Host Single-Cell
+and Microbial Transcriptomes.
+
+Pipeline: FASTQ → QC (fastp) → Align hg38 (Bowtie2) → Extract unmapped
+(samtools) → Classify (Kraken2) → Quantify (Bracken) → Visualize
+"""
+
+__version__ = "0.1.3"
+__author__ = "CellJanus Team"

celljanus-0.1.3/celljanus/__main__.py

@@ -0,0 +1,6 @@
+"""Allow running: python -m celljanus"""
+
+from celljanus.cli import main
+
+if __name__ == "__main__":
+    main()