Nullary

Nullary vs. DepMap

TLDR

  • DepMap (Cancer Dependency Map) is Broad Institute's flagship CRISPR screening dataset across 1000+ cell lines, maintained by Broad and Sanger
  • Nullary aggregates DepMap plus other CRISPR databases (BioGRID ORCS, GenomeCRISPR) and surfaces them alongside non-CRISPR negative data
  • DepMap is the right choice for deep dives into specific cell-line essentiality screens
  • Nullary is the right choice for cross-database CRISPR queries unified with other modalities

What each does

DepMap is a comprehensive CRISPR screening initiative covering essentiality, dependency, and synthetic lethality across ~1000 cancer cell lines. Includes per-guide fold changes, gene effect scores, and dependency annotations. Quarterly releases via depmap.org and bulk download.

Nullary aggregates CRISPR screen results from DepMap, BioGRID ORCS, and GenomeCRISPR into a unified schema, exposing them via MCP alongside non-CRISPR data (small molecules, antibodies, clinical trials).

When to use DepMap directly

  • You're doing dependency analysis on specific cancer cell lines
  • You need full per-cell-line, per-guide data with all quality metrics
  • You need synthetic lethality networks specific to DepMap's methodology
  • You're using DepMap-specific analysis tools (CRISPR-RBR, Achilles)

When to use Nullary

  • You want CRISPR data alongside other modalities for the same target
  • You want failed-guide annotations across multiple CRISPR databases (DepMap + BioGRID ORCS + GenomeCRISPR)
  • You want MCP-native access for agent workflows
  • You want alerts when new CRISPR failures appear in your target areas

Data overlap

Nullary's CRISPR modality includes DepMap as the primary source. We focus specifically on negative findings: failed guides, non-essential annotations, ancestry-specific failures. DepMap's full positive data isn't included (use DepMap directly for that).

A specific note

In 2024, Broad's analysis found that ~2% of DepMap guides systematically miss their targets in cells from certain ancestries. DepMap subsequently removed those guides from active screens. Nullary preserves the removed-guide annotations as failed_guide records — useful information for understanding screen limitations and avoiding similar issues in your own designs.

Bottom line

Use DepMap for deep cancer-dependency analysis. Use Nullary for cross-database CRISPR queries integrated with other modalities. The CRISPR data in Nullary cites back to DepMap with full provenance.