Results for “cellxgene”

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

XState Typegen

Use when triaging a study before any writing — stress-tests whether it clears Cell's bar (a complete, mechanistic, hypothesis-driven story with multiple converging lines of evidence) or belongs at a sibling. Use this first to decide Cell vs Molecular Cell vs Cell Reports vs Cell Reports Medicine before investing in framing or figures.

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills suite.

MaxFuse parameter tuning for datasets with large protein:RNA cell ratios (>100:1)

Write effective unit tests with modern MSTest 3.x/4.x, covering assertion APIs, data-driven tests, and test lifecycle best practices.

Runs and interprets Elixir/Phoenix tooling (mix test, credo, dialyzer, format), generates OTP-conforming modules, and helps with Ecto and LiveView patterns.

FREE — God-tier long-context memory for AI agents. Injects 500K-1M clean tokens, auto-summarizes with tone/intent preservation, compresses 14-turn history into 800 tokens.

Notebook Cell References

Specialist orchestrating codex exec / Antigravity CLI through dual paradigms — COMPETE (multi-variant comparison, select best) and COLLABORATE (decompose tasks across engines, integrate). Supports Solo/Team/Quick execution modes.

Use when parsing, extracting, or converting XML data from NCBI Entrez or other bioinformatics sources into tab-delimited tables. Use for selecting specific elements, filtering records, and restructuring hierarchical XML into flat formats for downstream analysis.

Use to finalize Cell Press display items — column-width sizing, minimum fonts, RGB, show-the-data with defined error bars/n/replicate type, scale bars, colorblind-safe palettes, multi-panel discipline, stand-alone legends, and image integrity.

Frangi vesselness 3D filter: Ra formula correction, scikit-image deprecations, GPU VRAM guard

FREE — God-tier long-context memory for AI agents. Injects 500K-1M clean tokens, auto-summarizes with tone/intent preservation, compresses 14-turn history into 800 tokens.

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.