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Verify cell identity. Direct cell differentiation.

Choose from three packages for cell identity assessment and in silico perturbation analysis. Optional add-ons cover sequencing, prep, and custom references.

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S010203N

Pick the package that fits your project.

01

CapybaraTM Benchmarking Analysis

Precise cell identity for up to two samples.

Up to 2 samples·1–2 weeks
02

Capybara Advanced Analysis

Benchmarking plus DEG/pathway analysis.

Up to 8 samples·2–3 weeks
03

CellOracleTM Differentiation Optimization Analysis

In silico perturbation screening to direct cell fate.

Up to 2 samples·2–4 weeks
01

Capybara · 1–2 weeks

CapybaraTM Benchmarking Analysis

Capybara Benchmarking gives precise cell identity information for up to two samples, especially in heterogeneous processes such as differentiation and reprogramming.

Max samples
Up to 2 samples
Per sample
50k cells/sample
Turnaround
1–2 weeks
  • Decomposes each cell into reference states, capturing partial reprogramming, transitional identities, and off-target fates.
  • Quantifies identity purity at single-cell resolution, showing how closely cells resemble the target type.
  • Reports mixed-identity and unclassified cells instead of forcing them into the nearest label.
  • Delivers one integrated report linking identity and composition across samples.
Start this package →See sample report (opens PDF in a new tab)

Package Snapshot

  1. 1-hour kickoff meeting to confirm goals and review sample details
  2. Cell Type Classification
  3. UMAP visualization for top ten cell types
  4. Differential Composition Analysis
  5. Multi-ID Analysis
  6. Identity Score Distributions
  7. Executive summary & next-step recommendations
  8. 1-hour consultation to review findings

You bring

  • Raw single-cell RNA-seq count matrix for up to 2 samples (up to 50k cells/sample).
  • A reference selected from CapyBio's curated list.
02

Capybara · 2–3 weeks

Capybara Advanced Analysis

Adds DEG and GSEA to Benchmarking, giving mechanistic context for time courses, protocol comparisons, and multi-condition experiments.

Max samples
Up to 8 samples
Per sample
50k cells/sample
Turnaround
2–3 weeks
  • Shows which genes and programs distinguish desired cells from off-target populations.
  • Connects cell identity to active biological pathways through curated gene sets.
  • Helps prioritize what to monitor next round: marker panels for qPCR, flow, or immunostaining.
  • Useful for identifying surface markers for downstream purification of selected populations.
  • Identifies pathways worth modulating through media, timing, or culture conditions.
  • Delivers one integrated report linking identity, composition, and transcriptional changes.
Start this package →See sample report (opens PDF in a new tab)

Package Snapshot

  1. 1-hour kickoff meeting to confirm goals and review sample details
  2. Cell Type Classification
  3. UMAP visualization for top ten cell types
  4. Differential Composition Analysis
  5. Multi-ID Analysis
  6. Identity Score Distributions
  7. Differentially Expressed Genes (DEG)
  8. Gene Set Enrichment Analysis (GSEA)
  9. Executive summary & next-step recommendations
  10. 1-hour consultation to review findings

You bring

  • Raw single-cell RNA-seq count matrix for up to 8 samples (up to 50k cells/sample).
  • A reference selected from CapyBio's curated list.
03

CellOracle · 2–4 weeks

CellOracleTM Differentiation Optimization Analysis

CellOracle uses curated gene regulatory networks to reveal the regulatory logic behind each cell state and rank the transcription factors most likely to shift fate.

Max samples
Up to 2 samples
Per sample
20k cells/sample
Turnaround
2–4 weeks
  • Simulates knockout and over-expression of 20 key TFs before wet-lab work, focusing effort on the strongest candidates.
  • Supports drug target discovery, disease modeling, cell engineering, and assay development.
  • Delivers one report covering GRN architecture, centrality comparisons, and ranked perturbation results.
Start this package →See sample report (opens PDF in a new tab)

Package Snapshot

  1. 1-hour kickoff meeting to confirm goals and review sample details
  2. Per-cluster network centrality (degree & eigenvector)
  3. Pairwise comparisons of key clusters
  4. In silico knockout + over-expression of 20 key TFs
  5. Executive summary & next-step recommendations
  6. 1-hour consultation to review findings

You bring

  • Pre-processed single-cell RNA-seq data for up to 2 samples (up to 20k cells/sample).
  • Cell clusters identified within each sample. No cross-sample clusters; ≥50 cells per cluster.
  • A 2D embedding for visualizing differentiation (e.g., UMAP or force atlas).
  • Pseudotime representing the differentiation trajectory from starting population toward target fate.
  • Three key clusters for pairwise centrality comparisons (typically target, starting, and major off-target).
  • One target cluster representing the desired end state, used to rank in silico perturbations.

Add-on modules

Bundle additional services with any package.

Add sequencing, data prep, extra samples, or custom reference work to any package.

Single-Cell RNA-seq

Library prep, QC, sequencing, and counts-matrix processing. Two-sample minimum; tiered by sample count.

Compatible with

All packages

Pre-Processing, Normalization & Clustering

Upstream preparation for CellOracle analysis. Batch normalization or correction can be scoped separately.

Compatible with

CellOracle Differentiation Optimization Analysis

DEG & GSEA Analysis

Adds differential expression and gene set enrichment to Capybara Benchmarking. Optional batch-effect correction.

Compatible with

Capybara Benchmarking Analysis

Additional Capybara Sample

Extend Benchmarking beyond 2 samples or Advanced beyond 8 samples.

Compatible with

Capybara Benchmarking & Advanced Analysis

Additional CellOracle Sample

Add samples beyond the 2 included in CellOracle Differentiation Optimization.

Compatible with

CellOracle Differentiation Optimization Analysis

Need something more custom? Let’s talk.

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