YuliaNuzhnenko/bioinformatics-agent-skills
Instructions file CodexOpenCode
Instructions for YuliaNuzhnenko/bioinformatics-agent-skills, covering agent integration & specification guide 🤖, 📌 supported agent host architectures, 🧪 skill frontmatter specification and 🔒 security & sandboxing.
YuliaNuzhnenko/bioinformatics-agent-skills
Instructions file
Instructions for YuliaNuzhnenko/bioinformatics-agent-skills, covering claude code project guidelines, project overview, development & validation commands and skill conventions.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Parses AlphaFold2 PDB files, computes per-residue pLDDT confidence scores, and evaluates Solvent Accessible Surface Area (SASA) of active site pockets.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Scans bacterial genome assemblies against CARD (Comprehensive Antibiotic Resistance Database) and ResFinder to map drug-class resistance heatmaps.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Runs DiffDock generative diffusion models for blind protein-ligand docking against AlphaFold structures and ranks candidates by confidence scores.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Parses multi-sample VCF files, queries Ensembl VEP REST API, filters ClinVar pathogenicity ratings, and maps driver mutations to FDA targeted drugs.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Executes GATK4 Mutect2 tumor-normal paired variant calling, applies LearnReadOrientationModel, and runs FilterMutectCalls for somatic SNV filtering.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Generates production Nextflow DSL2 process modules, handles tuple channel mapping, pins Docker containers, and configures AWS Batch / SLURM profiles.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Vectorizes PubMed abstracts using PubMedBERT, builds FAISS indices, and instructs agents to synthesize clinical evidence with exact PMID citations.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Automated negative binomial differential gene expression analysis, log2 fold-change calculation, p-value adjustment (FDR), and Volcano plot generation.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
DADA2 amplicon sequence variant (ASV) dereplication, Alpha/Beta diversity index calculation, SILVA taxonomy classification, and 3D PCoA projections.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Computes 2048-bit ECFP4 Morgan fingerprints from SMILES, trains LightGBM regressors for pIC50 prediction, and extracts SHAP feature attributions.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Autonomous single-cell RNA-seq quality control filtering, Harmony batch-effect correction, Leiden clustering, UMAP visualization, and marker gene annotation.
YuliaNuzhnenko/bioinformatics-agent-skills
Skill Claude CodeCodex
Downloads TCGA RNA-Seq datasets via TCGAbiolinks, normalizes log2(TPM+1) counts, and calculates tumor-infiltrating immune cell fractions (CIBERSORT).