Run or adapt a one-shot total RNA velocity workflow in `dynamo` for metabolic-labeling or scNT-seq `AnnData`, including monocle preprocessing with an optional curated gene list, grouped moments by labeling time, Model-2 `dynamics`, `calculate_velocity_alpha_minus_gamma_s`, low-dimensional projection with `cell_velocities`, and optional streamline or phase-portrait plotting. Use when converting tutorials such as `301_tutorial_hsc_velocity.ipynb`, or when choosing between `one_shot_method` branches like `sci_fate` and `combined` and projection `method` branches like `cosine` and `pearson`.
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Run or adapt a one-shot total RNA velocity workflow in `dynamo` for metabolic-labeling or scNT-seq `AnnData`, including monocle preprocessing with an optional curated gene list, grouped moments by labeling time, Model-2 `dynamics`, `calculate_velocity_alpha_minus_gamma_s`, low-dimensional projection with `cell_velocities`, and optional streamline or phase-portrait plotting. Use when converting tutorials such as `301_tutorial_hsc_velocity.ipynb`, or when choosing between `one_shot_method` branches like `sci_fate` and `combined` and projection `method` branches like `cosine` and `pearson`.
Dynamo One-Shot Total RNA Velocity
Goal
Run the stable execution spine behind the hematopoiesis scNT-seq tutorial: preprocess a one-shot labeling dataset, smooth by labeling time, force the Model-2 no-splicing branch for kinetics, compute total RNA velocity with alpha - gamma * s, then project that custom velocity to a low-dimensional embedding without treating the tutorial dataset as the workflow identity.
Quick Workflow
Inspect the input AnnData for new, total, and time, plus any reusable helpers such as uns["genes_to_use"] and obsm["X_umap"].
Preprocess with the monocle path. If a curated gene list exists, preserve it explicitly and use Preprocessor(force_gene_list=...) plus config_monocle_recipe(..., n_top_genes=len(gene_list)).
Materialize grouped moments with dyn.tl.moments(..., group='time') so the one-shot fit sees time-specific neighborhoods and creates M_n, M_t, and M_s.
Force the no-splicing Model-2 branch by setting adata.uns["pp"]["has_splicing"] = False, then run dyn.tl.dynamics(..., group='time', one_shot_method='sci_fate', model='deterministic') unless the user explicitly wants another branch.
Convert the fitted kinetic parameters into total RNA velocity with dyn.tl.calculate_velocity_alpha_minus_gamma_s(...).
Project the custom total RNA velocity with dyn.tl.cell_velocities(..., X=adata.layers["M_t"], V=adata.layers["velocity_alpha_minus_gamma_s"], method='cosine').
Treat streamline_plot and phase_portraits as optional visualization steps after velocity_umap already exists.
Interface Summary
Preprocessor.config_monocle_recipe(adata, n_top_genes=2000) configures the notebook-style monocle preprocessing path.
Preprocessor.preprocess_adata_monocle(adata, tkey=None, experiment_type=None) is the exact notebook entrypoint; Preprocessor.preprocess_adata(..., recipe='monocle', ...) is the higher-level wrapper.
dyn.tl.moments(..., group=None, use_gaussian_kernel=False, use_mnn=False, layers='all') creates smoothed first and second moments and stores obsp["moments_con"].
dyn.tl.dynamics(..., group=None, model='auto', est_method='auto', one_shot_method='combined', ...) estimates one-shot kinetic parameters and writes velocity-like layers such as velocity_N and velocity_T.
dyn.tl.calculate_velocity_alpha_minus_gamma_s(adata, gene_subset_key='use_for_pca', velocity_layer_name='velocity_alpha_minus_gamma_s') converts fitted rates plus M_n and M_s into the total RNA velocity layer used in the notebook.
dyn.tl.cell_velocities(..., X=None, V=None, basis='umap', method='pearson', adj_key='distances', enforce=False) projects the custom velocity to low-dimensional space and stores a kernel-specific transition matrix.
dyn.pl.streamline_plot(..., basis='umap', method='gaussian') and dyn.pl.phase_portraits(...) are optional presentation entrypoints after the analytical path is complete.
Read references/source-grounding.md before documenting narrower parameter behavior than the live source currently supports.
Branch Selection
Use the curated-gene-list branch when uns["genes_to_use"] or a user-supplied marker/HVG list exists. Preserve that list explicitly before subsetting or concatenating because anndata.concat(...) can drop it.
Use recipe='monocle' for this workflow family. Other recipe branches are real source-level options, but the total-RNA one-shot path here was empirically checked only on the monocle branch.
Use group='time' on moments(...) and dynamics(...) unless the user explicitly wants to smooth and fit without time-specific neighborhoods.
Use one_shot_method='sci_fate' for notebook parity and one_shot_method='combined' when the user explicitly wants the steady-state-plus-absolute-gamma branch. Both were empirically checked.
Use model='deterministic' by default for this total-RNA workflow. If the user wants a splicing-aware or stochastic branch, stop and switch to a different workflow instead of silently mixing models.
Use cell_velocities(..., method='cosine') for notebook-style total-RNA projection. Use method='pearson' when the user wants the alternate kernel with a different transition-matrix key. Treat kmc, fp, and transform as advanced branches with extra assumptions.
Use streamline_plot(..., method='gaussian') for default streamline rendering. Switch to method='SparseVFC' only after a vector field has been reconstructed and the user explicitly wants that rendering path.
Read references/branch-selection.md before choosing non-default recipe, one_shot_method, model, method, or plotting branches.
Input Contract
Expect a metabolic-labeling AnnData with usable new and total layers and a labeling-time column.
Expect the time column to be accessible as adata.obs["time"] before calling calculate_velocity_alpha_minus_gamma_s(...), or rename / copy the user's time key to time.
Treat spliced and unspliced as optional inputs for the raw object, not as the target model branch. The notebook-compatible total-RNA path forces has_splicing=False before dynamics(...).
Expect M_n, M_t, and M_s to be created by moments(...) before calling calculate_velocity_alpha_minus_gamma_s(...).
Expect a valid embedding such as X_umap plus a matching adjacency matrix under obsp["distances"] before calling cell_velocities(...).
Treat tutorial-specific fields such as genes_to_use, cell_type, and the hematopoiesis sample layout as worked examples, not universal defaults.
Minimal Execution Patterns
For the notebook-compatible one-shot total RNA workflow:
the function reports each unique time point it processed
After cell_velocities(...), check these items:
adata.obsm["velocity_umap"] exists for the default UMAP branch
adata.obsp["cosine_transition_matrix"] exists for method='cosine'
adata.obsp["pearson_transition_matrix"] exists for method='pearson'
Constraints
Do not treat velocity_T from dynamics(...) as the notebook endpoint. The tutorial's total-RNA visualization path depends on the extra calculate_velocity_alpha_minus_gamma_s(...) plus cell_velocities(...) steps.
Do not forget to rename or copy the time column to adata.obs["time"] before calculate_velocity_alpha_minus_gamma_s(...); current source hard-codes that key.
Do not assume uns["genes_to_use"] survives AnnData concatenation or subsetting workflows. Preserve it explicitly when reconstructing subsets.
Do not keep has_splicing=True if the goal is Model-2 total RNA velocity. Preprocessing auto-detects splicing and labeling together on the hematopoiesis raw object.
Do not interpret one_shot_method from adata.uns["dynamics"]; current runtime does not store it there.
Do not make small per-time groups the default. Reviewer runs with fewer than 50 cells per time group emitted NaN-velocity warnings and filtered genes before projection.
Resource Map
Read references/branch-selection.md for decision rules across recipe, grouped smoothing, one_shot_method, and projection method branches.
Read references/visualization-and-phase-portraits.md when the user explicitly wants notebook-style streamlines or total-RNA phase-portrait adaptation.
Read references/source-grounding.md for inspected signatures, source-level branch evidence, and empirical execution notes.
Read references/source-notebook-map.md to see how docs/tutorials/notebooks/301_tutorial_hsc_velocity.ipynb was converted into this reusable skill.
Read references/compatibility.md when notebook wording and current source behavior diverge.
