ODODlabOmics Deconvolution Lab

Scientific Workspace

Omics Deconvolution Lab

ODlab consolidates strict data validation, model registry orchestration, execution tracking, and report-ready outputs into a professional local-first research environment.

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Integrated Models

10

Bulk and spatial methods are registered from the manifest.

Bulk Models

5

Reference-guided deconvolution for bulk RNA-seq.

ST Models

5

Spot-level spatial composition inference.

Two Analysis Entrances

Bulk Deconvolution

Upload a single-cell reference and bulk expression matrix, choose a model, and obtain cell-type fractions, summary tables, and downloadable artifacts.

Launch Bulk Analysis

Spatial Transcriptomics

Upload ST expression with optional coordinates and tissue image, run a spatial model, and review spot-level results with indexed outputs and logs.

Launch ST Analysis

Input Standards

  • Reference and bulk or spatial expression matrices are validated as structured `.h5ad` AnnData objects.
  • Spatial coordinate files must use the required barcode and pixel coordinate header order.
  • Tissue images are treated as optional downstream overlays and stored within the task workspace.

Execution Design

Manifest-driven registry keeps model metadata separate from platform code.
Every task stores uploads, logs, parameters, results, and exportable reports by task ID.
Running status, validation readiness, and result indexing stay consistent across workflows.

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Recommended Public Data Sources

Bulk Database

GEO / NCBI

Public gene expression database for bulk RNA-seq and microarray data.

https://www.ncbi.nlm.nih.gov/geo/info/download.html

Bulk Database

TCGA / GDC Data Portal

Cancer bulk RNA-seq data portal.

https://portal.gdc.cancer.gov/

Bulk Database

GTEx Portal

RNA-seq datasets for normal human tissues.

https://www.gtexportal.org/home/datasets

Bulk Database

recount3

Uniformly processed human and mouse RNA-seq resources.

https://rna.recount.bio/

Bulk Database

ArrayExpress / BioStudies

EBI functional genomics entry point with RNA-seq datasets.

https://www.ebi.ac.uk/biostudies/arrayexpress

ST Database

10x Genomics Datasets

Official 10x datasets including Visium spatial transcriptomics.

https://www.10xgenomics.com/datasets

ST Database

10x Visium HD Example Data

Official Visium HD example data.

https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data

ST Database

spatialLIBD

Human DLPFC 10x Visium spatial transcriptomics data.

https://research.libd.org/spatialLIBD/

ST Database

STOmicsDB

Integrated spatial transcriptomics database.

https://db.cngb.org/stomics/

ST Database

SOAR

Spatial transcriptomics data search and analysis resource.

https://soar.fsm.northwestern.edu/