Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/cellgeni/nf-scvi-metrics

Grid search to optimise hyperparameters for scVI

https://github.com/cellgeni/nf-scvi-metrics

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Grid search to optimise hyperparameters for scVI

Basic Info
  • Host: GitHub
  • Owner: cellgeni
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 34.2 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

scVI Hyperparameter Metrics Pipeline

This pipeline performs a grid search to optimize hyperparameters for scVI. The grid is constructed by combining elements from predefined lists of model input parameters. After running scVI with each set of parameters, integration metrics are calculated using scib-metrics.

Repository Contents

  • main.nf – The Nextflow pipeline that orchestrates the entire workflow.
  • nextflow.config – Configuration file that:
    • Submits processes to LSF on Sanger's HPC.
    • Ensures the correct environment is set via a Singularity container (absolute path).
    • Defines global default parameters.
  • examples/inputs.py – Example .py file specifying the path to anndata and configurations for scVI and scib-metrics.
  • examples/run_scVI_metrics.sh – Example script to execute the pipeline.
  • Dockerfile – Defines a Docker image with scVI and scib-metrics version 0.2.2.

Pipeline Arguments

  • --input_file – Path to a .py file specifying:
    • The path to anndata.
    • Configuration details for scVI and scib-metrics.

Optional parameters:

  • --help — Display this help message
  • --umap — Set this flag to calculate umap

Owner

  • Name: Cellular Genetics Informatics
  • Login: cellgeni
  • Kind: organization
  • Location: United Kingdom

Wellcome Sanger Institute

GitHub Events

Total
  • Member event: 1
  • Push event: 12
  • Pull request event: 1
  • Create event: 3
Last Year
  • Member event: 1
  • Push event: 12
  • Pull request event: 1
  • Create event: 3

Dependencies

Dockerfile docker
  • python 3.11 build