Results for “stannp”

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data through clustering, cell-type annotation, DE, or pseudotime workflows; for building or reading the .h5ad data structure itself (layers, obs/var, concatenation, backed mode) prefer alterlab-anndata instead, and for RNA velocity from spliced/unspliced counts prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

Configures, troubleshoots, and extends NPSP Customizable Rollups, including rollup definitions, filter groups, batch job modes, and migration from legacy rollups.

Manage Node.js dependencies with pnpm, including workspaces, catalogs, patches, and supply-chain security.

How MaksPM hands off work to agents using sessions_spawn for continuous pipeline flow, with file-reference pattern for preserving full project specs. Updated 2026-03-21 with 9-phase pipeline and Forge architecture phase.

Use when filtering `RNAsubopt -s` output to keep p-optimal RNA structures in a ViennaRNA post-processing pipeline.

Manages Node.js dependencies with strict resolution, workspaces, catalogs, patches, and overrides, including CI/CD setup and migration guidance.