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Deconvolve โ€” fast, explainable deconvolution for bulk & spatial omics

Get accurate cell-type proportions and high-resolution cellular maps with validated algorithms, scalable pipelines, and reproducible outputs ready for publication.

Features

Core features

Validated Algorithms

Ensemble methods combining marker-based, reference-free, and single-cell guided models for robust cell-type proportion estimates across platforms.

Scalable Pipelines

Cloud-native workflows with batch processing, parallelization, and automatic checkpointing for large cohorts and spatial experiments.

Explainability & QC

Per-sample confidence metrics, marker contribution reports, and interactive QC dashboards to support reproducibility and publications.

How it works

How Deconvolve works

  1. Upload bulk or spatial expression matrices and optional single-cell references or marker lists.
  2. Select workflow: reference-guided, semi-supervised, or reference-free. Customize parameters or use curated presets.
  3. Run the pipeline on cloud or on-premise. Monitor progress and inspect intermediate diagnostics.
  4. Download cell-type proportion matrices, spatial maps, and publication-ready visualizations.
Interactive results explorer

Use cases

Common use cases

Tissue heterogeneity in disease

Quantify immune infiltration and stromal composition across diseased and healthy cohorts to identify cellular correlates of clinical outcomes.

Spatial transcriptomics

Resolve mixed spots into high-resolution cellular maps to study spatial organization, microenvironments, and cellโ€“cell interactions.

Integrations & pipelines

Seamless export for Seurat, Scanpy, Bioconductor, and interoperable outputs (CSV, AnnData, SingleCellExperiment).

Regulatory & translational analytics

Validated QC and audit trails for translational studies, cohort stratification, and biomarker discovery.

Integrations & API

Integrations & API

Plug Deconvolve into your existing workflows. We provide REST APIs, Nextflow/CWL modules, and SDKs for Python and R.

API-first

Programmatic submission, status polling, and artifact retrieval for automation and reproducible pipelines.

SDKs

Python and R clients with helpers to convert Seurat/Scanpy objects and visualize results directly in notebooks.

Cloud & On-prem

Deploy on managed cloud, private VPC, or run locally with containerized tooling and provenance tracking.

Pricing & Trial

Pricing

Flexible pricing for academic labs, core facilities, and enterprise โ€” pay-as-you-go compute, subscriptions for teams, and discounts for academic users.

Academic

Free*

Access core workflows, community support, and limited compute credits for publications and validation.

Request Access

Team

Monthly

Collaboration features, priority compute, and shared project spaces for research groups.

Start Trial

Enterprise

Custom

On-prem deployments, dedicated SLAs, and compliance packages for regulated studies.

Contact Sales

*Academic tier requires affiliation verification.

Get started

Get started with Deconvolve