Skills by risk · page 292
Highest-trust agent skills
9,826 skills rated SAFE with grade A or B, best score first. All are grade B today: grade A needs a sandboxed run we do not do for skills yet. Ties are broken by stars, so a repository with many skills can fill a page.
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ModelsAtlas. “Highest-trust agent skills”. Retrieved 30 Oct 2026. https://modelsatlas.com/skills/trusted/page/292
GPTomics/bioSkills
Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity…
GPTomics/bioSkills
Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs…
GPTomics/bioSkills
Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event).…
GPTomics/bioSkills
Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing…
GPTomics/bioSkills
a set of SKILLS.md for doing bioinformatics with agents like claude code
GPTomics/bioSkills
Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction…
GPTomics/bioSkills
Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters),…
GPTomics/bioSkills
Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or…
GPTomics/bioSkills
Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and…
GPTomics/bioSkills
Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick…
GPTomics/bioSkills
Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural…
GPTomics/bioSkills
Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for…
GPTomics/bioSkills
Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines…
GPTomics/bioSkills
Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON…
GPTomics/bioSkills
Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-grammar) or the unmaintained UpSetR, with explicit cardinality vs degree sorting, attribute panels,…
GPTomics/bioSkills
Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE),…
GPTomics/bioSkills
Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution…
GPTomics/bioSkills
Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking,…
GPTomics/bioSkills
a set of SKILLS.md for doing bioinformatics with agents like claude code
charleswiltgen/axiom
Use when implementing, testing, or evaluating ANY Apple Intelligence, on-device AI, or speech-to-text feature. Covers Foundation Models, @Generable, LanguageModelSession, Tool protocol, eval suites, model-as-judge…
matlab/simulink-agentic-toolkit
Builds and edits Simulink, System Composer, Stateflow, and Simscape models. Use when modifying model structure, parameters, ports, connections, or Stateflow chart internals.
matlab/simulink-agentic-toolkit
Generate a standalone bug report that another developer can use to reproduce, investigate, and fix an issue. Use when the user says 'file a bug', 'write a bug report', 'report this issue', or asks to document a defect…
matlab/simulink-agentic-toolkit
Configures Simulink simulations non-destructively using SimulationInput objects — parameter overrides without modifying the model, batch sweeps via parsim, custom input signals via Dataset, and simulation data retrieval…
matlab/simulink-agentic-toolkit
Specify algorithms for Model-Based Design: system specs, architecture specs, implementation plans, test plans. Use when creating specifications for controllers, signal processing, diagnostics, estimators, or other…