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scFoundry
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scFoundry

Introduction

  • How scFoundry works

Getting started

  • Installation
  • The workspace
  • Downloading model weights
  • Quickstart

Preparing your data

  • Input data format
  • Demo datasets

Tasks

  • Tasks
  • Embed
  • Transfer
  • Fine-tune
  • Benchmark
  • Geometry

Reference

  • Command reference
  • Supported methods
  • Parameter reference
  • Output reference
  • nextflow.config reference

Running at scale

  • Running on an HPC cluster
  • GPU memory and runtime
  • Troubleshooting

Benchmark results

  • Benchmark results
  • Results explorer
  • What the geometry says

Extending

  • Extending scFoundry
  • Adding a method
  • Contributing a method

Reproducing the paper

  • Reproducing the paper
  • Benchmark design
  • Evaluation metrics
  • Representation-geometry probes

About

  • Citation
  • Changelog
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