YuliaNuzhnenko
- 12 skills
- 0 followers
- 21 hours ago last updated
- ▌ Card Amr Profiler · yulianuzhnenkoScans bacterial genome assemblies against CARD (Comprehensive Antibiotic Resistance Database) and ResFinder to map drug-class resistance heatmaps.
- ▌ Pydeseq2 Bulk Rna · yulianuzhnenkoAutomated negative binomial differential gene expression analysis, log2 fold-change calculation, p-value adjustment (FDR), and Volcano plot generation.
- ▌ Scanpy Sc Analyzer · yulianuzhnenkoAutonomous single-cell RNA-seq quality control filtering, Harmony batch-effect correction, Leiden clustering, UMAP visualization, and marker gene annotation.
- ▌ Qiime2 16s Microbiome · yulianuzhnenkoDADA2 amplicon sequence variant (ASV) dereplication, Alpha/Beta diversity index calculation, SILVA taxonomy classification, and 3D PCoA projections.
- ▌ Tcga Cibersort Deconv · yulianuzhnenkoDownloads TCGA RNA-Seq datasets via TCGAbiolinks, normalizes log2(TPM+1) counts, and calculates tumor-infiltrating immune cell fractions (CIBERSORT).
- ▌ Pubmed RAG Synthesizer · yulianuzhnenkoVectorizes PubMed abstracts using PubMedBERT, builds FAISS indices, and instructs agents to synthesize clinical evidence with exact PMID citations.
- ▌ Nextflow Dsl2 Generator · yulianuzhnenkoGenerates production Nextflow DSL2 process modules, handles tuple channel mapping, pins Docker containers, and configures AWS Batch / SLURM profiles.
- ▌ Rdkit Qsar Pharmacophore · yulianuzhnenkoComputes 2048-bit ECFP4 Morgan fingerprints from SMILES, trains LightGBM regressors for pIC50 prediction, and extracts SHAP feature attributions.
- ▌ Diffdock Virtual Screener · yulianuzhnenkoRuns DiffDock generative diffusion models for blind protein-ligand docking against AlphaFold structures and ranks candidates by confidence scores.
- ▌ Alphafold Pocket Evaluator · yulianuzhnenkoParses AlphaFold2 PDB files, computes per-residue pLDDT confidence scores, and evaluates Solvent Accessible Surface Area (SASA) of active site pockets.
- ▌ Gatk4 Somatic Variant Caller · yulianuzhnenkoExecutes GATK4 Mutect2 tumor-normal paired variant calling, applies LearnReadOrientationModel, and runs FilterMutectCalls for somatic SNV filtering.
- ▌ Ensembl Vep Variant Annotator · yulianuzhnenkoParses multi-sample VCF files, queries Ensembl VEP REST API, filters ClinVar pathogenicity ratings, and maps driver mutations to FDA targeted drugs.