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SkillsMP has collected 9 skills from aristoteleo/dynamo-release. Open a skill to review its source and details.
Showing 9 of 9 collected skills.
Perform in silico gene perturbation on a dynamo vector-field AnnData to predict cell fate diversion after single or multi-gene activation or suppression, then visualize the results with streamline or quiver plots. Use when running dyn.pd.perturbation,…
Compute least action paths (LAP) between hematopoietic or general cell types in a dynamo vector-field AnnData, then rank transcription factors by MSD along each path and evaluate predictions via ROC analysis. Use when running…
Run or adapt a conventional spliced/unspliced RNA velocity workflow in `dynamo`, including `Preprocessor` preprocessing, `dynamics`, low-dimensional `cell_velocities`, `VectorField`, topology / potential analysis, confidence-based correction, fate prediction,…
Run downstream differential-geometry analysis on a `dynamo` vector-field `AnnData`, including velocity, acceleration, curvature, Jacobian, regulatory-network, ddhodge pseudotime, and state-graph branches. Use when adapting the…
Convert Ensembl-style gene IDs to gene symbols in `dynamo` with `dynamo.preprocessing.convert2gene_symbol` or `dynamo.preprocessing.convert2symbol`, including human and zebrafish IDs, version-suffix stripping, `AnnData.var_names` updates, and optional…
Compare lineage appearance timing and its regulators on a precomputed `dynamo` vector-field `AnnData` using topography, graph potentials, Jacobian, and vector-calculus outputs. Use when checking whether one lineage appears earlier than its peers, curating…
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`,…
Run or adapt dynamo preprocessing with `dynamo.preprocessing.Preprocessor`, including the `recipe` branches `monocle`, `seurat`, `sctransform`, `pearson_residuals`, and `monocle_pearson_residuals`. Use when converting or reproducing…
Convert pseudotime into reusable `dynamo` RNA velocity outputs on an `AnnData` object, then optionally continue into vector field, topology / potential, fate, and animation without relying on measured spliced/unspliced kinetics. Use when adapting the…