Skip to content

Quickstart Demo And Expected Outputs

This page shows the full prep -> run -> eval command flow for the public cSCC demo and the expected output layout. For the public release, the prepared demo bundle and example outputs are distributed separately from git through a Google Drive download link. After extracting that bundle, the expected layout should start under:

demo_runs/cscc_demo/

The shipped demo uses the real P6_vis_rep1 fixture and the example config set under configs/examples/cscc_demo/. The demo dataset ID used in the commands below is P6_vis_rep1.

Before You Start

  1. Install the controller environment
  2. Prepare method runtime environments
  3. Download the external tools and reference data
  4. Download the public demo bundle
  5. Use the provided demo configs

The default public demo enables CopyKAT, so it does not require allele-aware reference bundles or external tool source trees.

Demo Bundle

Download the packaged cSCC demo bundle from:

The unpacked bundle should provide the demo_runs/cscc_demo/ layout referenced below.

Included Example Outputs

The packaged example run can be used as a reference for the expected directory layout. Key subdirectories include:

  • demo_runs/cscc_demo/processed_data/P6_vis_rep1/
  • demo_runs/cscc_demo/raw_results/P6_vis_rep1/CopyKAT/
  • demo_runs/cscc_demo/evaluation/P6_vis_rep1/

Step 1: Prepare Data

Run:

st-cnvbench --steps prep \
  --data-config configs/examples/cscc_demo/data.yaml \
  --prep-ids P6_vis_rep1

Check the prepared dataset under:

demo_runs/cscc_demo/processed_data/P6_vis_rep1/

Expected outputs include:

  • filtered_feature_bc_matrix/
  • filtered_feature_bc_matrix.h5ad
  • spatial/tissue_positions.csv
  • metadata_P6_vis_rep1_tumor_normal.tsv

Step 2: Run A Model

Example with CopyKAT in conda mode:

st-cnvbench --steps run \
  --data-config configs/examples/cscc_demo/data.yaml \
  --model-config configs/examples/cscc_demo/models.yaml \
  --prep-ids P6_vis_rep1 \
  --exec-mode conda \
  --models CopyKAT

Check raw model outputs under:

demo_runs/cscc_demo/raw_results/P6_vis_rep1/CopyKAT/

Important files to inspect:

  • CopyKAT_run.log
  • CopyKAT_run.perf
  • P6_vis_rep1_copykat_prediction.txt
  • P6_vis_rep1_copykat_CNA_results.txt
  • copykat_subcluster_results.txt

Step 3: Evaluate

Run:

st-cnvbench --steps eval \
  --data-config configs/examples/cscc_demo/data.yaml \
  --eval-config configs/examples/cscc_demo/eval.yaml \
  --prep-ids P6_vis_rep1 \
  --models CopyKAT \
  --eval-tasks cnv_profile

Check evaluation outputs under:

demo_runs/cscc_demo/evaluation/P6_vis_rep1/

For the default demo command above, the main task output is under:

demo_runs/cscc_demo/evaluation/P6_vis_rep1/cnv_profile/

Typical outputs include:

  • metrics summary tables
  • CNV profile plots
  • karyogram-level comparison plots
  • per-method exported CNV profile tables

Full Demo Command

If you want to run all three stages in one command, use:

st-cnvbench \
  --steps prep run eval \
  --data-config configs/examples/cscc_demo/data.yaml \
  --model-config configs/examples/cscc_demo/models.yaml \
  --eval-config configs/examples/cscc_demo/eval.yaml \
  --prep-ids P6_vis_rep1 \
  --exec-mode conda \
  --models CopyKAT \
  --eval-tasks cnv_profile

Try Next