OmniBioAI

Single-Cell Analysis (Seurat)

Guided clustering (v1): QC → LogNormalize → HVG → PCA → Louvain → UMAP → Markers. Supports CellRanger MTX, CellRanger H5, and alevin-fry.

Plugin: single_cell_analysis Engine: local Upload limit: 4096 MB

{# ----------------------------------------- 1) Create Run (Registry or Upload) ------------------------------------------ #}

Choose input type and source. The run will stage inputs under work/runs/single_cell_analysis/<run_id>/in/.

Input type

MTX/alevin-fry typically arrive as archives; H5 can be a direct .h5 or an archive containing it.

Source

Registry Upload

Select object

Tip: If your dataset is a folder on disk, register it as a directory-like object; otherwise use an archive/H5.

Reset

After creating a run, go to the results page and click “Execute” (or wire an execute button later).

{# ----------------------------------------- 2) Upload & Register (optional helper) ------------------------------------------ #}

Upload a dataset and (best-effort) register it into the Object Registry so it appears in the dropdown next time.

If you upload MTX/alevin-fry, prefer archiving the *folder* so detection works (see logs if it fails).

{# ----------------------------------------- What will be produced (v1) ------------------------------------------ #}