# YuliaNuzhnenko

> Open-source publisher. Listings imported from github.com/YuliaNuzhnenko — credited to the original author with their license.

- **Listings:** 12
- **Total installs:** 0
- **Profile:** https://agentstack.voostack.com/s/yulianuzhnenko
- **Website:** https://github.com/YuliaNuzhnenko

## Published listings

- [Scanpy Sc Analyzer](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-scanpy-sc-analyzer) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-scanpy-sc-analyzer`
  Autonomous single-cell RNA-seq quality control filtering, Harmony batch-effect correction, Leiden clustering, UMAP visualization, and marker gene annotation.
- [Alphafold Pocket Evaluator](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-alphafold-pocket-evaluator) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-alphafold-pocket-evaluator`
  Parses AlphaFold2 PDB files, computes per-residue pLDDT confidence scores, and evaluates Solvent Accessible Surface Area (SASA) of active site pockets.
- [Pubmed Rag Synthesizer](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-pubmed-rag-synthesizer) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-pubmed-rag-synthesizer`
  Vectorizes PubMed abstracts using PubMedBERT, builds FAISS indices, and instructs agents to synthesize clinical evidence with exact PMID citations.
- [Diffdock Virtual Screener](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-diffdock-virtual-screener) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-diffdock-virtual-screener`
  Runs DiffDock generative diffusion models for blind protein-ligand docking against AlphaFold structures and ranks candidates by confidence scores.
- [Pydeseq2 Bulk Rna](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-pydeseq2-bulk-rna) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-pydeseq2-bulk-rna`
  Automated negative binomial differential gene expression analysis, log2 fold-change calculation, p-value adjustment (FDR), and Volcano plot generation.
- [Gatk4 Somatic Variant Caller](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-gatk4-somatic-variant-caller) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-gatk4-somatic-variant-caller`
  Executes GATK4 Mutect2 tumor-normal paired variant calling, applies LearnReadOrientationModel, and runs FilterMutectCalls for somatic SNV filtering.
- [Ensembl Vep Variant Annotator](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-ensembl-vep-variant-annotator) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-ensembl-vep-variant-annotator`
  Parses multi-sample VCF files, queries Ensembl VEP REST API, filters ClinVar pathogenicity ratings, and maps driver mutations to FDA targeted drugs.
- [Qiime2 16s Microbiome](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-qiime2-16s-microbiome) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-qiime2-16s-microbiome`
  DADA2 amplicon sequence variant (ASV) dereplication, Alpha/Beta diversity index calculation, SILVA taxonomy classification, and 3D PCoA projections.
- [Rdkit Qsar Pharmacophore](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-rdkit-qsar-pharmacophore) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-rdkit-qsar-pharmacophore`
  Computes 2048-bit ECFP4 Morgan fingerprints from SMILES, trains LightGBM regressors for pIC50 prediction, and extracts SHAP feature attributions.
- [Tcga Cibersort Deconv](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-tcga-cibersort-deconv) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-tcga-cibersort-deconv`
  Downloads TCGA RNA-Seq datasets via TCGAbiolinks, normalizes log2(TPM+1) counts, and calculates tumor-infiltrating immune cell fractions (CIBERSORT).
- [Nextflow Dsl2 Generator](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-nextflow-dsl2-generator) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-nextflow-dsl2-generator`
  Generates production Nextflow DSL2 process modules, handles tuple channel mapping, pins Docker containers, and configures AWS Batch / SLURM profiles.
- [Card Amr Profiler](https://agentstack.voostack.com/l/skill-yulianuzhnenko-bioinformatics-agent-skills-card-amr-profiler) — Skill · Free · security-reviewed — `agentstack add skill-yulianuzhnenko-bioinformatics-agent-skills-card-amr-profiler`
  Scans bacterial genome assemblies against CARD (Comprehensive Antibiotic Resistance Database) and ResFinder to map drug-class resistance heatmaps.

---
Seller on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Install any with `agentstack add <slug>`.