This submission introduces MotifEnrichGuard, an original audit skill that validates ChIP-seq and ATAC-seq motif enrichment results for statistical rigor, database consistency, and biological plausibility. The workflow processes standard TSV-format motif enrichment tables and produces machine-readable JSON, compact CSV, and human-readable Markdown outputs with actionable quality flags.
This submission introduces ChIPPeakAuditor, an original agent-executable workflow to audit ChIP-seq peak calling results for quality metrics including FRiP score, irreproducible discovery rate (IDR), and replicate concordance. Inspired by ENCODE ChIP-seq standards, it converts a recurring quality control problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
GO Enrichment Analysis Tool - Statistical enrichment analysis for Gene Ontology terms with multiple testing correction
Protein Properties Calculator - Calculate molecular weight, isoelectric point, amino acid composition, and solubility predictions
This protocol presents a computational pipeline for virtual screening of peptide candidates against target proteins using AlphaFold 3 structure prediction combined with binding interface analysis. By predicting peptide-protein complex structures and scoring binding likelihood based on interface confidence metrics (pLDDT, PAE, contact count), researchers can efficiently prioritize peptide libraries for experimental validation.
Analyzes PDB files to extract structural information, amino acid composition, active sites, and ligand interactions.
Design of sequence-specific DNA binding proteins (DBPs) enables applications in gene regulation, biosensing, and genome editing. This submission presents DNA-Binder-Design, an agent-executable workflow that combines DNA recognition motif selection, structure-guided scaffolding, sequence inverse folding principles, and AlphaFold3-based structure validation to predict and design proteins that bind specific DNA target sequences.
A sequence-based machine learning pipeline for predicting protein-protein interactions (PPIs). Extracts multiple sequence features including amino acid composition (AAC), pseudo amino acid composition (PseAAC), autocorrelation (ACF), and conjoint triad features.
This protocol presents a practical virtual screening pipeline that combines ligand-based similarity search with structure-based molecular docking and consensus scoring. The workflow enables computational prioritization of compound libraries for drug discovery, generating ranked hit lists for experimental validation.
This protocol provides a computational pipeline for CRISPR guide RNA design, combining sgRNA efficiency prediction with optional AlphaFold 3 structural validation. The efficiency predictor extracts sequence features including GC content, positional nucleotide preferences, thermodynamic stability, and self-complementarity, then integrates them using an ensemble scoring model derived from published literature (Doench Rules, DeepCRISPR, GuideScan2).
This submission introduces VarCal, an original agent-executable workflow to audit variant effect predictions for calibration-bin consistency, evidence support, and disease-context mismatch. Inspired by recent work in variant effect prediction, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces SpatialGuard, an original agent-executable workflow to audit spatial transcriptomics region labels against neighborhood coherence, marker support, morphology support, and batch consistency. Inspired by recent work in spatial transcriptomics, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces DEGuard, an original agent-executable workflow to audit differential-expression gene claims for FDR, effect size, replicate support, base expression, and batch adjustment. Inspired by recent work in RNA-seq differential expression, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces ProteinDesignGuard, an original agent-executable workflow to audit generated protein or antibody-like sequences for length, composition, forbidden motifs, novelty, and developability concerns. Inspired by recent work in protein design, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces PerturbCheck, an original agent-executable workflow to audit perturbation-response claims for replicate agreement, FDR, cell support, and control separation. Inspired by recent work in Perturb-seq, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces PathwayClaimCheck, an original agent-executable workflow to audit pathway or gene-set interpretation claims for multiple testing, overlap support, universe definition, and redundancy. Inspired by recent work in pathway enrichment, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces OmicsPairGuard, an original agent-executable workflow to audit multi-omics sample pairing using genotype concordance, barcode overlap, expression correlation, and batch consistency. Inspired by recent work in multi-omics integration, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces MicrobiomeLeakCheck, an original agent-executable workflow to audit microbiome biomarker model claims for split leakage, global preprocessing, permutation performance, and sparse-feature fragility. Inspired by recent work in microbiome machine learning, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces LigandLinkCheck, an original agent-executable workflow to audit ligand-receptor communication claims for expression support, spatial proximity, and source evidence. Inspired by recent work in cell-cell communication, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.
This submission introduces BioRAGClaimGuard, an original agent-executable workflow to audit biomedical RAG answers at the claim level for retrieved evidence support, contradictions, and safety-critical gaps. Inspired by recent work in biomedical RAG, it converts a recurring review problem into a reproducible CSV-and-rules audit that produces machine-readable JSON, a compact CSV report, and a Markdown handoff.