Results for “sui”

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differentiation dynamics from spliced/unspliced layers (velocyto/STARsolo output); for the general QC, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for .h5ad data-structure I/O and layer wrangling prefer alterlab-anndata instead. Part of the AlterLab Academic Skills suite.

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.

Submits and tracks protein-testing experiments on the Adaptyv Bio Foundry cloud lab (wet-lab validation), and optimizes protein sequences before submission with computational tools (NetSolP, SoluProt, SolubleMPNN, ESM). Use when designing proteins that need wet-lab validation - binding/affinity screening, expression testing, thermostability, or fluorescence assays - or when submitting experiments to the Foundry API, browsing the target catalog, tracking experiment status, retrieving results, or pre-screening sequences for solubility/expression. Triggers on "Adaptyv", "Foundry API", "cloud lab", "biolayer interferometry / BLI", "wet-lab validation". Part of the AlterLab Academic Skills suite.

Security controls for RAG. Indirect prompt-injection via retrieved documents, PII detection/redaction (Microsoft Presidio, AWS Comprehend), multi-tenant isolation, ACL-aware retrieval with row-level/metadata filtering, data-leakage prevention, jailbreak hardening on retrieved context, GDPR right-to-be-forgotten in vector DBs. USE WHEN: user mentions "prompt injection RAG", "indirect prompt injection", "PII redaction", "Presidio", "ACL RAG", "row-level security", "multi-tenant RAG isolation", "GDPR vector DB", "right to be forgotten", "jailbreak", "data leakage RAG" DO NOT USE FOR: hallucination detection - use `rag-guardrails`; tenancy scaling patterns - use `rag-production`; audit tracing schema - use `rag-observability`

Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links; designed for lychee-based GitHub Actions link checkers but generalizes to markdown-link-check and similar tools. Use when the request mentions link audit, dead links, link health, lychee, broken links, link checker, markdown link audit, link-health audit, 404 audit, check-links failing, CI link-check, or 連結健檢, 死鏈, 失效連結, 斷鏈檢查. Part of the AlterLab Academic Skills suite.

Use when the user requests diagrams, flowcharts, architecture diagrams, ER diagrams, UML / sequence / class diagrams, SysML / MBSE diagrams (block definition, internal block, requirement, parametric), BPMN business process diagrams, swimlane / cross-functional flowcharts, network topology, cloud architecture from Terraform or Kubernetes manifests, ML/DL model figures (Transformer/CNN/LSTM), mind maps, or any visualization. Also use proactively when explaining systems with 3+ components, complex data flows, or relationships that benefit from visual representation. Best suited when the diagram needs custom styling, rich shape vocabulary, swimlanes, or exportable images (PNG/SVG/PDF/JPG). Generates .drawio XML and exports locally via the native draw.io desktop CLI.

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Operate Firebase from the terminal with `firebase-tools`: install/auth the CLI, bootstrap `firebase.json` / `.firebaserc`, run the Emulator Suite, deploy Hosting / Functions / rules / App Hosting, manage preview channels, and handle Firebase admin tasks like auth import/export, Remote Config, App Distribution, and Extensions. Use when the job is Firebase platform/project operation through the CLI. Triggers on: firebase deploy, firebase init, firebase emulators, firebase hosting, firebase functions, firebase firestore, firebase database, firebase auth import, firebase remote config, firebase app distribution, firebase extensions, firebase apphosting, firebase dataconnect, firebase cli, firebase-tools, deploy firebase, firebase preview channel, firebase login, firebase use, firebase target apply. Route backend AI workflow orchestration to `genkit` and direct in-app SDK integration to `genkit` (`client-ai-logic` mode).

Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk-of-bias assessment, meta-analysis, APA 7.0 report compilation, editorial and devil's-advocate review, ethics review, and post-research literature monitoring. Use when the request mentions research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, or 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題. Part of the AlterLab Academic Skills suite.

Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or "QC" a data file, or to understand its structure/content/quality before deciding what analysis to run. Covers tabular (.csv .tsv .xlsx .parquet), arrays (.npy .npz .hdf5 .h5 .mat .fits), sequence/genomics (.fasta .fastq .sam .bam .vcf .bed .gff .gtf .h5ad), microscopy (.tif .nd2 .czi .lif .ims .dcm .nii), spectroscopy/MS (.mzML .mzXML .mgf .fid .jdx), chemistry (.pdb .cif .mol .sdf .xyz .gro), and proteomics/metabolomics (.pepXML .mzid .mzTab). For zero-shot forecasting of a series use alterlab-timesfm; to create/configure a chunked cloud array store use alterlab-zarr. Part of the AlterLab Academic Skills suite.