Rdkit Qsar Pharmacophore
Computes 2048-bit ECFP4 Morgan fingerprints from SMILES, trains LightGBM regressors for pIC50 prediction, and extracts SHAP feature attributions.
Pydeseq2 Bulk Rna
Automated negative binomial differential gene expression analysis, log2 fold-change calculation, p-value adjustment (FDR), and Volcano plot generation.
Qiime2 16s Microbiome
DADA2 amplicon sequence variant (ASV) dereplication, Alpha/Beta diversity index calculation, SILVA taxonomy classification, and 3D PCoA projections.
Scanpy Sc Analyzer
Autonomous single-cell RNA-seq quality control filtering, Harmony batch-effect correction, Leiden clustering, UMAP visualization, and marker gene annotation.
Diffdock Virtual Screener
Runs DiffDock generative diffusion models for blind protein-ligand docking against AlphaFold structures and ranks candidates by confidence scores.
Tcga Cibersort Deconv
Downloads TCGA RNA-Seq datasets via TCGAbiolinks, normalizes log2(TPM+1) counts, and calculates tumor-infiltrating immune cell fractions (CIBERSORT).
Card Amr Profiler
Scans bacterial genome assemblies against CARD (Comprehensive Antibiotic Resistance Database) and ResFinder to map drug-class resistance heatmaps.
Nextflow Dsl2 Generator
Generates production Nextflow DSL2 process modules, handles tuple channel mapping, pins Docker containers, and configures AWS Batch / SLURM profiles.
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
Parses multi-sample VCF files, queries Ensembl VEP REST API, filters ClinVar pathogenicity ratings, and maps driver mutations to FDA targeted drugs.
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
Vectorizes PubMed abstracts using PubMedBERT, builds FAISS indices, and instructs agents to synthesize clinical evidence with exact PMID citations.