---
title: "Provenance-backed single-cell and biomedical benchmark enrichment batch."
task: ""
lineage_type: import
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.benchmark-v2.yml
upstream_sha: 7a064bf0
imported_at: 2026-08-08
prompt_class: catalogue
upstream_changes: accepted
author: upstream
validated: false
---

# Provenance-backed single-cell and biomedical benchmark enrichment batch.
resources:
  scmulan:
    entities: [cell, gene]
    methods: [language-model, transformer]
    modalities: [epigenomics, multi-omics, proteomics, single-cell-rna-seq, transcriptomics]
    tasks: [foundation-model-pretraining, representation-learning]
    github: https://github.com/SuperBianC/scMulan
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/SuperBianC/scMulan

  proteingym:
    entities: [protein]
    modalities: [protein-sequence]
    tasks: [regression]
    github: https://github.com/OATML-Markslab/ProteinGym
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/OATML-Markslab/ProteinGym

  lincs_l1000:
    entities: [cell, compound, gene]
    modalities: [transcriptomics]
    tasks: [perturbation-prediction]
    last_checked: 2026-08-08
    metadata_sources:
      - https://lincsproject.org/LINCS/tools/workflows/find-the-best-place-to-obtain-the-lincs-l1000-data

  prism:
    entities: [cell, drug]
    tasks: [drug-response-prediction]
    last_checked: 2026-08-08
    metadata_sources:
      - https://depmap.org/portal/prism/

  pharmgkb:
    entities: [drug, gene, phenotype, variant]
    modalities: [clinical, genomics]
    tasks: [drug-response-prediction]
    last_checked: 2026-08-08
    metadata_sources:
      - https://www.pharmgkb.org/