qcp-omics 0.2.0

Quality control, preprocessing and analysis of omics data for machine learning

QCP-Omics

Installation

From PyPI

Requires Python version >= 3.11.

1. Create a virtual environment: python3 -m venv .venv
2. Activate it: source .venv/bin/activate
3. Install the tool: pip install qcp-omics
4. Verify installation: qcp

Singularity (on HPC) - recommended

1. Load singularity: module load singularity
2. Pull the image from docker: singularity pull qcp-omics.sif docker://georgelepsaya/qcp-omics:latest
3. Verify installation: singularity run qcp-omics.sif

Instructions

will be added later

{
  "dataset_type": "clinical | genomics | proteomics",
  "dataset_path": "dataset/path.csv | .tsv",
  "metadata_path": "metadata/path",
  "output_path": "output/path",
  "features_cols": false,
  "en_header": true,
  "is_raw": true,
  "steps_to_run": ["step 1", "step 2"],
  "dtypes": {
    "feature1": "type",
    "feature2": "type"
  }
}