semvec/pypi-packages huggingface dataset:
omicscheck 1.0.2
A lightweight tool to inspect GEO series matrices online before downloading.
Requires Python: >=3.8


# OmicsCheck: Intelligent Quality Assessment for Gene Expression Data

**OmicsCheck** is a cutting-edge, automated tool designed to evaluate the quality of gene expression datasets from GEO (Gene Expression Omnibus). It intelligently analyzes raw expression matrices and generates professional PDF reports, visual summaries, and interpretable quality metrics – enabling researchers to screen studies before conducting downstream analysis.

---

##  Features

-  **Download and parse** GEO Series Matrix files automatically.
-  **Auto-orientation** of matrices (genes × samples vs. samples × genes).
-  **Log2 transformation suggestions** based on data distribution.
-  **Data filtering** for the most variable genes (top-N).
-  **QA Score Evaluation** using multi-criteria assessment.
-  **PCA and Heatmap visualization** of gene-level variability.
-  **PDF report generation** with visual plots and summary stats.
-  **Exports analysis files** in `.json` and `.csv` formats.

---

##  Installation

```bash
pip install omicscheck
```

> Requires Python 3.8+

---

##  Usage

```bash
omicscheck run GSE12345
```

This will:

1. Download the matrix file for `GSE12345`
2. Parse and analyze the data
3. Evaluate quality and suggest improvements
4. Generate visual plots
5. Create a full PDF report at: `~/Desktop/OmicsCheck/GSE12345/report.pdf`

---

##  Quality Evaluation Logic

OmicsCheck uses a composite QA Score based on:

- Matrix completeness
- Distribution characteristics
- Gene variance
- Sample PCA spread

Each dataset receives a final **Rating**: `Excellent`, `Good`, `Moderate`, or `Poor`

---

##  Output Files

- `report.pdf`: Professional scientific report
- `analysis.json`: Full results in machine-readable format
- `analysis.csv`: Simplified metrics table
- `boxplot.png`, `heatmap.png`, `pca_plot.png`: Generated plots

---

##  Example Output

Example report: `docs/report_example.pdf`

---

# OmicsCheck

A smart pre-download screening tool for high-quality omics datasets.

[![PyPI version](https://img.shields.io/pypi/v/OmicsCheck.svg)](https://pypi.org/project/OmicsCheck/)
[![License](https://img.shields.io/badge/license-MIT-blue.svg)](./LICENSE)
[![DOI](https://img.shields.io/badge/DOI-10.21203/rs.3.rs--7297713--v1-blue)](https://doi.org/10.21203/rs.3.rs-7297713/v1)

---

##  Citation

> Ahmed Yassin. *OmicsCheck Enables Improved Selection of High-Quality Gene Expression Datasets: A Pre-download Screening Tool with Biological Impact Assessment*.  
> Research Square (2025).  
> [https://doi.org/10.21203/rs.3.rs-7297713/v1](https://doi.org/10.21203/rs.3.rs-7297713/v1)


---

##  Contributing

We welcome contributions! Fork the repo and submit a pull request.

---

##  Contact

Lead Developer: [AHMED YASSIN || Computational Biologist]  
Email: [Ahmedyassin300@outlook.com]  
Project Page: [https://github.com/AHMEDY3DGENOME/OmicsCheck]

---

© 2025 OmicsCheck Team. All rights reserved.
kres 1.0.1
Kubernetes Resource Restarter
Requires Python: >=3.7

# Kubernetes-Restarter

Kubernetes-Restarter (`kres`) is a CLI tool for safely restarting Kubernetes resources (pods, deployments, statefulsets) based on secret or configmap changes.

## Features

- Restart pods, deployments, or statefulsets referencing specific secrets/configmaps
- Check access permissions for Kubernetes resources
- Modular, extensible CLI structure
- Colorful logging with multiple log levels

## Installation

1. **Clone the repository:**
   ```
   git clone https://github.com/ShashankPalla2002/Kubernetes-Restarter.git
   cd Kubernetes-Restarter
   ```

2. **Install dependencies:**
   ```
   pip install -r requirements.txt
   ```

## Usage

Run the CLI tool:
```
python -m kres.main <command> [options]
```

### Commands

- **init**  
  Initialize with a kubeconfig and start the Kres API.
  ```
  python -m kres.main init --kubeconfig ~/.kube/config --port 5454 --log INFO
  ```

- **logout**  
  Logout and clear session data.
  ```
  python -m kres.main logout --log INFO
  ```

- **api**  
  Check status of Kres API or Kubernetes API.
  ```
  python -m kres.main api --type kres --log INFO
  python -m kres.main api --type kubernetes --log INFO
  ```

- **access**  
  Check if kres can access a resource in a namespace.
  ```
  python -m kres.main access --namespace default --resource pods --verb get --log INFO
  ```

- **restart**  
  Restart resources referencing a secret/configmap.
  ```
  python -m kres.main restart --namespace default --resource deployments --all --secret mysecret --reason "Secret updated" --log INFO
  python -m kres.main restart --namespace default --resource pods --name mypod --log INFO
  ```

## Configuration

- **Kubeconfig:**  
  By default, kres uses `~/.kube/config`. You can specify a different path with `--kubeconfig`.
- **Port:**  
  Kres API runs on port `5454` by default. Use `--port` to change.

## Logging

- Log levels: `DEBUG`, `INFO`, `WARNING`, `ERROR`
- Color-coded output for better readability

## Project Structure

```
kres/
  api/
    apiHandler.py
    kresApi.py
    kresApiLauncher.py
  config/
    extractConfig.py
    loadConfig.py
  encryption/
    tokenEncryption.py
  subparsers/
    accessParser.py
    apiParser.py
    logoutParser.py
    restartParser.py
  utils/
    extractResourceNames.py
    logger.py
    parser.py
  main.py
README.md
requirements.txt
```

## Contributing

Pull requests and issues are welcome! Please open an issue to discuss major changes.
python-sixel-windows 0.2.1
Display images in the terminal
Requires Python: >=3.0
Keywords: image, sixel, terminal

# python-sixel

Display images in the terminal using [Sixel](https://en.wikipedia.org/wiki/Sixel).

This is a fork of [PySixel](https://github.com/lubosz/python-sixel) to add windows compatibility.

Check [arewesixelyet.com](https://www.arewesixelyet.com/) for supported terminals.

## Installation

### PyPI release
```
pip install python_sixel_windows
```



```python
import sys
from sixel import converter

c = converter.SixelConverter("foo.png")
c.write(sys.stdout)
```

See examples directory for more examples.

## sixelconv

python-sixel provides a command line tool.

Display an image in the terminal
```
sixelconv [options] filename
```

Or by using a pipe
```
cat filename | sixelconv [options]
```

### Options

```
-h, --help                                            show this help message and exit
-8, --8bit-mode                                       Generate a sixel image for 8bit terminal or printer
-7, --7bit-mode                                       Generate a sixel image for 7bit terminal or printer
-r, --relative-position                               Treat specified position as relative one
-a, --absolute-position                               Treat specified position as absolute one
-x LEFT, --left=LEFT                                  Left position in cell size, or pixel size with unit 'px'
-y TOP, --top=TOP                                     Top position in cell size, or pixel size with unit 'px'
-w WIDTH, --width=WIDTH                               Width in cell size, or pixel size with unit 'px'
-e HEIGHT, --height=HEIGHT                            Height in cell size, or pixel size with unit 'px'
-t ALPHATHRESHOLD, --alpha-threshold=ALPHATHRESHOLD   Alpha threshold for PNG-to-SIXEL image conversion
-c, --chromakey                                       Enable auto chroma key processing
-n NCOLOR, --ncolor=NCOLOR                            Specify number of colors
-b, --body-only                                       Output sixel without header and DCS envelope
-f, --fast                                            The speed priority mode (default)
-s, --size                                            The size priority mode
```

### Examples

View an image file
```
sixelconv test.png
```

Generate sixel file from an image file
```
sixelconv < test.png > test.six
```

View generated sixel file
```
cat test.six
```