SCUBA

Instead of clustering cells, SCUBA groups co-expressed genes into automatically annotated modules, then shows how their activity shifts between conditions.

How it works

For each cell type, SCUBA holds a reference gene co-expression network, built from single-cell data in the CZ CELLxGENE Discover Census. Genes that rise and fall together across cells form a module; each module is annotated with the biological process it most likely represents — drafted by a large language model from its genes, then reviewed and approved by a domain expert — and modules connect to one another by correlation. In the app, each node is a module and each edge a correlation; double-clicking a module opens the network of its genes.

When a single-cell dataset is analysed, SCUBA aggregates its cells per sample and cell type and compares module and gene activity between the dataset's own conditions — for example inflamed vs uninflamed tissue — with per-sample statistics behind every difference.

What is in the reference atlas

28 cell types, 3,171 gene modules and 11,230 genes.

Cell type	Modules	Genes	Description
CD19⁺ B cells	97	1,387	Antigen-specific lymphocytes bearing surface immunoglobulin; after germinal-centre selection they class-switch, mutate their receptors, and mature into memory cells or antibody-secreting plasma cells.
CD4⁺ T cells	149	2,742	Helper T lymphocytes recognising peptide on MHC class II; differentiate into Th1, Th17, Tfh, or regulatory subsets that orchestrate antibody production, phagocyte activation, and mucosal tolerance.
CD8⁺ T cells	89	1,070	Cytotoxic T lymphocytes recognising peptide on MHC class I; release perforin and granzymes to kill infected or transformed cells, and persist as tissue-resident memory in mucosa.
Colonocytes	145	3,635	Absorptive columnar epithelium of the colon; they reclaim water and electrolytes, oxidise microbial butyrate for energy, and form the tight-junction barrier separating the microbiota from the tissue.
Colorectal carcinoma	91	1,016	Malignant epithelial cells arising from colorectal crypts through stepwise APC, KRAS, and TP53 lesions; they show aberrant Wnt activity, invade the stroma, and remodel the immune microenvironment.
Dendritic cells	154	3,517	Professional antigen-presenting sentinels sampling the lumen and lamina propria; on activation they migrate to lymph nodes and prime naive T cells, setting immunity or tolerance.
Endothelial	143	2,287	Vascular lining cells forming the blood–tissue interface; they control perfusion, permeability, and coagulation, and display adhesion molecules that recruit circulating leukocytes into inflamed mucosa.
Enterocytes	101	1,052	Absorptive columnar epithelium of the small intestine; brush-border enzymes and transporters digest and absorb nutrients and bile acids, and lipids are packaged into chylomicrons for lymphatic export.
Fibroblasts	129	1,785	Mesenchymal stromal cells producing collagen and matrix; they define tissue architecture, supply niche factors to epithelium and immune cells, and drive fibrosis when chronically activated.
Gamma-delta T cells	187	3,937	Unconventional T cells with γδ receptors and little MHC restriction; enriched at epithelial surfaces, they sense stress ligands and respond immediately with cytotoxicity and IL-17.
Glial cells	73	786	Enteric glia derived from neural crest, ensheathing the gut’s intrinsic neurons; they support neurotransmission, reinforce barrier function, and modulate motility and mucosal immune signalling.
Goblet cells	99	1,112	Secretory epithelial cells packed with mucin granules; they build the layered mucus barrier, deliver antigen to dendritic cells, and release trefoil peptides that support epithelial repair.
Hematopoietic progenitor cells	69	815	Bone-marrow-derived multipotent precursors circulating at low frequency; retain self-renewal and lineage plasticity, seeding tissues to replenish myeloid and lymphoid compartments during inflammation, injury, and steady-state turnover.
Innate lymphoid cells	101	2,159	Tissue-resident lymphocytes without antigen receptors, mirroring helper T subsets; responding to epithelial alarmins, they secrete cytokines that sustain barrier integrity, antimicrobial defence, and lymphoid tissue organisation.
Intestinal stem cells and transit amplifying cells	96	1,084	Crypt-base stem cells and their rapidly dividing transit-amplifying progeny; sustained by Wnt and Notch signals, they renew the entire epithelium every few days and regenerate it after injury.
Lymphatic endothelial	96	1,240	Endothelium of lymphatic capillaries and collectors; they drain interstitial fluid, absorb lipids, and guide dendritic cells and lymphocytes toward draining lymph nodes via chemokine gradients.
Macrophages	150	4,314	Long-lived mononuclear phagocytes replenished from monocytes; clear apoptotic cells and microbes, sample luminal antigen, and secrete cytokines that shape tissue repair, fibrosis, and mucosal tolerance.
Mast cells	189	4,145	Tissue-resident granulocytes derived from bone marrow progenitors, storing histamine and proteases; IgE crosslinking triggers rapid degranulation, driving allergy, parasite defence, and innate mucosal immune regulation.
Microfold-like cells	109	1,231	Specialised follicle-associated epithelial cells with sparse microvilli; they transcytose luminal antigens and microbes to underlying lymphoid tissue, initiating mucosal IgA responses and immune surveillance.
Monocytes	101	1,113	Circulating bone-marrow-derived phagocytes recruited rapidly to inflamed mucosa; they engulf pathogens, present antigen, release inflammatory mediators, then differentiate locally into macrophages or dendritic cells.
Mucosal-associated invariant T cell	143	2,318	Semi-invariant T cells restricted by MR1, recognising bacterial riboflavin metabolites; enriched in mucosa and liver, they respond rapidly with cytotoxicity and IL-17, bridging innate and adaptive immunity.
Natural Killer cells	88	934	Cytotoxic innate lymphocytes lacking rearranged antigen receptors; integrate activating and inhibitory signals to kill stressed, virally infected, or MHC-low tumour cells and secrete interferon-gamma.
Neutrophils	72	820	Short-lived granulocytes, the first responders mobilised from marrow; kill microbes through phagocytosis, reactive oxygen, and extracellular traps, at the cost of collateral tissue damage.
Pericytes	78	813	Contractile mural cells embracing capillaries within the basement membrane; they stabilise vessels, tune microvascular tone and permeability, and can be recruited into fibrotic and angiogenic programmes.
Plasma cells	69	1,272	Terminally differentiated B cells with expanded secretory machinery; in gut mucosa they secrete dimeric IgA transported into the lumen, neutralising microbes and shaping the microbiota.
Plasmacytoid dendritic cells	142	2,912	Rare lymphoid-like dendritic cells sensing nucleic acids through endosomal TLR7 and TLR9; they secrete copious type I interferon, driving antiviral defence and, when dysregulated, autoimmunity.
Smooth muscle cells	124	1,528	Contractile mesenchymal cells forming the gut wall muscularis layers; rich in actin-myosin filaments, they drive peristaltic contraction, regulate motility, and modulate stromal and inflammatory signalling.
Tuft cells	87	1,014	Rare chemosensory epithelial cells with apical microvillar tufts; using taste-receptor signalling they detect helminths and protists, releasing IL-25 to launch type 2 immunity.

Example datasets

The public version opens on three published datasets:

Colorectal cancer — Pelka et al.

Mismatch-repair-deficient vs proficient tumours; tumour vs adjacent tissue.

COVID-19, sepsis and influenza — COMBAT cohort

Severe vs mild disease; influenza vs COVID-19; septic or not.

Inflammatory bowel disease — TAURUS cohort

Ulcerative colitis vs Crohn's disease; before and after anti-TNF therapy.

Using SCUBA

Open SCUBA in a desktop browser. Every dataset, cell type and module can be explored interactively: search a gene, colour the network by a contrast between conditions, and inspect per-sample differences behind each result.