LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
multibench/__init__.py
multibench/__main__.py
multibench/_compat.py
multibench/cli.py
multibench/config.py
multibench/discover.py
multibench/workflow.py
multibench/data/__init__.py
multibench/data/catalog.py
multibench/data/fetch.py
multibench/data/results.py
multibench/engine/__init__.py
multibench/engine/builder.py
multibench/engine/env_groups.yaml
multibench/engine/env_specs.yaml
multibench/engine/envs.py
multibench/engine/ingest.py
multibench/engine/io.py
multibench/engine/methods.yaml
multibench/engine/output_urls.json
multibench/engine/packed_sizes.json
multibench/engine/packed_urls.json
multibench/engine/params.yaml
multibench/engine/references.yaml
multibench/engine/registry.py
multibench/engine/resolve.py
multibench/engine/runner.py
multibench/engine/runtimes.yaml
multibench/engine/schema.py
multibench/engine/upstream.py
multibench/engine/upstream_knobs.yaml
multibench/engine/drivers/run_concerto.py
multibench/engine/drivers/run_matilda.py
multibench/engine/drivers/run_stabmap.R
multibench/engine/env_locks/MOFA2_env.yml
multibench/engine/env_locks/env_moETM.yml
multibench/engine/env_locks/env_sciPENN.yml
multibench/engine/env_locks/glue.yml
multibench/engine/env_locks/matilda.post.sh
multibench/engine/env_locks/matilda.yml
multibench/engine/env_locks/scmb_cobolt3.post.sh
multibench/engine/env_locks/scmb_cobolt3.yml
multibench/engine/env_locks/scmb_concerto.yml
multibench/engine/env_locks/scmb_ipolng2.yml
multibench/engine/env_locks/scmb_mira.yml
multibench/engine/env_locks/scmb_multigrate2.yml
multibench/engine/env_locks/scmb_multivi.yml
multibench/engine/env_locks/scmb_r.post.sh
multibench/engine/env_locks/scmb_r.yml
multibench/engine/env_locks/scmb_scican.yml
multibench/engine/env_locks/scmb_scjoint.yml
multibench/engine/env_locks/scmb_scmdc.yml
multibench/engine/env_locks/scmb_scmm2.yml
multibench/engine/env_locks/scmb_scmsi.yml
multibench/engine/env_locks/scmb_scmvp4.post.sh
multibench/engine/env_locks/scmb_scmvp4.yml
multibench/engine/env_locks/scmb_scvi.yml
multibench/engine/env_locks/scmb_seurat4b.yml
multibench/engine/env_locks/scmb_seurat5.yml
multibench/engine/env_locks/scmb_torch.post.sh
multibench/engine/env_locks/scmb_torch.yml
multibench/engine/env_locks/scmb_torch_v2.post.sh
multibench/engine/env_locks/scmb_torch_v2.yml
multibench/engine/env_locks/scmb_vimcca.yml
multibench/engine/env_locks/scmb_vipcca27.yml
multibench/engine/env_locks/unitednet.yml
multibench/eval/__init__.py
multibench/eval/io.py
multibench/eval/pipeline.py
multibench/eval/scib.py
multibench/files/README_PROVENANCE.txt
multibench/files/dataset.csv
multibench/files/method.csv
multibench/files/metric_full.csv
multibench/plot/__init__.py
multibench/plot/bar.py
multibench/plot/bubble.py
multibench/plot/style.py
multibench/result/rerun/long_all_D11.csv
multibench/result/rerun/long_all_D11s.csv
multibench/result/rerun/long_all_D28.csv
multibench/result/rerun/long_all_D28s.csv
multibench/result/rerun/long_all_D45.csv
multibench/result/rerun/long_all_D45s.csv
multibench/result/rerun/long_all_D52.csv
multibench/result/rerun/long_all_D52s.csv
multibench/result/scib_metric/cross integration/D52/scMoMaT/metric.csv
multibench/result/scib_metric/diagonal integration/D24/Conos/metric.csv
multibench/result/scib_metric/diagonal integration/D24/Conos/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/Conos/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/Conos/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/Conos/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/GLUE/metric.csv
multibench/result/scib_metric/diagonal integration/D24/GLUE/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/GLUE/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/GLUE/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/GLUE/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/MultiMAP/metric.csv
multibench/result/scib_metric/diagonal integration/D24/MultiMAP/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/MultiMAP/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/MultiMAP/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/MultiMAP/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/Portal/metric.csv
multibench/result/scib_metric/diagonal integration/D24/Portal/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/Portal/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/Portal/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/Portal/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/SCALEX/metric.csv
multibench/result/scib_metric/diagonal integration/D24/SCALEX/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/SCALEX/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/SCALEX/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/SCALEX/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v3/metric.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v3/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v3/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v3/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v3/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v5/metric.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v5/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v5/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v5/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/Seurat_v5/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/VIPCCA/metric.csv
multibench/result/scib_metric/diagonal integration/D24/VIPCCA/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/VIPCCA/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/VIPCCA/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/VIPCCA/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/iNMF/metric.csv
multibench/result/scib_metric/diagonal integration/D24/iNMF/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/iNMF/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/iNMF/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/iNMF/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/online_iNMF/metric.csv
multibench/result/scib_metric/diagonal integration/D24/online_iNMF/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/online_iNMF/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/online_iNMF/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/online_iNMF/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/scBridge/metric.csv
multibench/result/scib_metric/diagonal integration/D24/scBridge/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/scBridge/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/scBridge/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/scBridge/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/scJoint/metric.csv
multibench/result/scib_metric/diagonal integration/D24/scJoint/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/scJoint/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/scJoint/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/scJoint/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/sciCAN/metric.csv
multibench/result/scib_metric/diagonal integration/D24/sciCAN/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/sciCAN/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/sciCAN/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/sciCAN/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D24/uniPort/metric.csv
multibench/result/scib_metric/diagonal integration/D24/uniPort/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D24/uniPort/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D24/uniPort/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D24/uniPort/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/Conos/metric.csv
multibench/result/scib_metric/diagonal integration/D25/Conos/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/Conos/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/Conos/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/Conos/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/GLUE/metric.csv
multibench/result/scib_metric/diagonal integration/D25/GLUE/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/GLUE/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/GLUE/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/GLUE/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/MultiMAP/metric.csv
multibench/result/scib_metric/diagonal integration/D25/MultiMAP/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/MultiMAP/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/MultiMAP/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/MultiMAP/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/Portal/metric.csv
multibench/result/scib_metric/diagonal integration/D25/Portal/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/Portal/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/Portal/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/Portal/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/SCALEX/metric.csv
multibench/result/scib_metric/diagonal integration/D25/SCALEX/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/SCALEX/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/SCALEX/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/SCALEX/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v3/metric.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v3/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v3/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v3/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v3/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v5/metric.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v5/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v5/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v5/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/Seurat_v5/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/VIPCCA/metric.csv
multibench/result/scib_metric/diagonal integration/D25/VIPCCA/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/VIPCCA/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/VIPCCA/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/VIPCCA/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/iNMF/metric.csv
multibench/result/scib_metric/diagonal integration/D25/iNMF/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/iNMF/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/iNMF/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/iNMF/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/online_iNMF/metric.csv
multibench/result/scib_metric/diagonal integration/D25/online_iNMF/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/online_iNMF/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/online_iNMF/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/online_iNMF/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/scBridge/metric.csv
multibench/result/scib_metric/diagonal integration/D25/scBridge/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/scBridge/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/scBridge/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/scBridge/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/scJoint/metric.csv
multibench/result/scib_metric/diagonal integration/D25/scJoint/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/scJoint/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/scJoint/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/scJoint/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/sciCAN/metric.csv
multibench/result/scib_metric/diagonal integration/D25/sciCAN/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/sciCAN/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/sciCAN/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/sciCAN/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D25/uniPort/metric.csv
multibench/result/scib_metric/diagonal integration/D25/uniPort/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D25/uniPort/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D25/uniPort/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D25/uniPort/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/Conos/metric.csv
multibench/result/scib_metric/diagonal integration/D28/Conos/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/Conos/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/Conos/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/Conos/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/GLUE/metric.csv
multibench/result/scib_metric/diagonal integration/D28/GLUE/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/GLUE/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/GLUE/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/GLUE/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/MultiMAP/metric.csv
multibench/result/scib_metric/diagonal integration/D28/MultiMAP/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/MultiMAP/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/MultiMAP/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/MultiMAP/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/Portal/metric.csv
multibench/result/scib_metric/diagonal integration/D28/Portal/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/Portal/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/Portal/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/Portal/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/SCALEX/metric.csv
multibench/result/scib_metric/diagonal integration/D28/SCALEX/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/SCALEX/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/SCALEX/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/SCALEX/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v3/metric.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v3/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v3/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v3/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v3/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v5/metric.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v5/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v5/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v5/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/Seurat_v5/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/VIPCCA/metric.csv
multibench/result/scib_metric/diagonal integration/D28/VIPCCA/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/VIPCCA/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/VIPCCA/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/VIPCCA/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/iNMF/metric.csv
multibench/result/scib_metric/diagonal integration/D28/iNMF/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/iNMF/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/iNMF/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/iNMF/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/online_iNMF/metric.csv
multibench/result/scib_metric/diagonal integration/D28/online_iNMF/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/online_iNMF/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/online_iNMF/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/online_iNMF/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/scBridge/metric.csv
multibench/result/scib_metric/diagonal integration/D28/scBridge/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/scBridge/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/scBridge/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/scBridge/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/scJoint/metric.csv
multibench/result/scib_metric/diagonal integration/D28/scJoint/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/scJoint/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/scJoint/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/scJoint/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/sciCAN/metric.csv
multibench/result/scib_metric/diagonal integration/D28/sciCAN/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/sciCAN/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/sciCAN/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/sciCAN/metric_louvain.csv
multibench/result/scib_metric/diagonal integration/D28/uniPort/metric.csv
multibench/result/scib_metric/diagonal integration/D28/uniPort/metric_ari_nmi_batch.csv
multibench/result/scib_metric/diagonal integration/D28/uniPort/metric_asw_iasw_if1.csv
multibench/result/scib_metric/diagonal integration/D28/uniPort/metric_kmeans.csv
multibench/result/scib_metric/diagonal integration/D28/uniPort/metric_louvain.csv
multibench/result/scib_metric/vertical integration/D11/Multigrate/metric.csv
multibench/result/scib_metric/vertical integration/D11/moETM/metric.csv
multibench/result/scib_metric/vertical integration/D11/scMM/metric.csv
multibench/result/scib_metric/vertical integration/D11/scMSI/metric.csv
multibench/result/scib_metric/vertical integration/D11/scMoMaT/metric.csv
multibench/result/scib_metric/vertical integration/D11/sciPENN/metric.csv
multibench_sc.egg-info/PKG-INFO
multibench_sc.egg-info/SOURCES.txt
multibench_sc.egg-info/dependency_links.txt
multibench_sc.egg-info/entry_points.txt
multibench_sc.egg-info/requires.txt
multibench_sc.egg-info/top_level.txt