Results for “scvelo”

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

Scaffolds or audits Zod-validated environment variables for a Next.js service, including src/lib/env.ts, .env.example, scripts/check-env.ts, and pnpm check:env. Use when adding env vars, auditing process.env usage, or aligning with deployment secrets.

Operates Scaleway cloud resources through the scw CLI, covering instances, images, object storage, Kubernetes, and databases.

Bootstraps a local Python environment for a skill package by creating a venv and installing dependencies with a stdlib-only script.

Audit environment-variable hygiene and secrets safety across local development and production with practical scanning, drift awareness, and rotation readiness.

Generates backend source code files, .env.example, and pr-description.md from BA, TechLead, and PM artifacts, following a configurable seniority level.

Deploy applications and manage projects with complete CLI reference. Commands for deployments, projects, domains, environment variables, and live documentation access.

Scan container images for known vulnerabilities using Anchore Grype with SBOM-based matching and configurable severity thresholds.

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.