Results for “allele-genotyping”

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.

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.

Operate and extend barretlee/agent-pulse, the evidence-backed AI industry intelligence system: inspect source catalog and lifecycle, collect and normalize signals, bind evidence, cluster Events, evaluate system health, generate Scout hypotheses, export the privacy-safe public site, and verify release gates. Use when the user asks to run, configure, debug, extend, or explain Agent Pulse, its collectors, Control Room, narratives, Scout, or GitHub Pages output. Triggers on: agent-pulse, Agent Pulse, evidence-backed intelligence, source catalog, signal collection, Event clustering, source audit, Scout opportunity, public export, weekly brief, or AI industry intelligence pipeline.

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.

Configure Gemini and Codex CLI tools with Cloudflare AI Gateway endpoints and MCP servers.

Stand up a self-hostable, typo-tolerant search environment with Typesense — the open-source Algolia / ElasticSearch alternative (single C++ binary, <50ms instant search, no runtime deps). One routing-first skill: pick a server mode (binary download, official Docker image, or managed Typesense Cloud), install an API client (Python/JS/PHP/Ruby official; Go/Dart/C# community), design a collection schema, index documents, and run searches with typo tolerance, faceting/filtering, geo-search, sorting, grouping, synonyms, curation, scoped API keys, and federated multi-search — then wire an InstantSearch.js UI and a Raft-based HA cluster for production. Use when the user wants to build or operate an installable search backend, add site/app/product search, or migrate off Algolia/Elasticsearch. Triggers on: typesense, search engine, typo-tolerant search, algolia alternative, elasticsearch alternative, instantsearch, faceted search, geo search, vector search, self-hosted search, site search, product search.

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.