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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Longitudinal Monitoring--> --- name: bio-longitudinal-monitoring description: Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutation clearance kinetics, and defines molecular response criteria. Use when monitoring patients during therapy or detecting molecular relapse before clinical progression. tool_type: python primary_tool: pandas measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. al...Votes: 0GitHub stars: 6
- Methylation Based Detection--> --- name: bio-methylation-based-detection description: Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for early cancer detection or minimal residual disease. tool_type: python primary_tool: MethylDackel measurable_outcome: Execute skill workflow successfully with valid output within 15 mi...Votes: 0GitHub stars: 6
- Tumor Fraction Estimation--> --- name: bio-tumor-fraction-estimation description: Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA percentage. Requires 0.1-1x sWGS coverage. Use when quantifying tumor burden from liquid biopsy or monitoring treatment response. tool_type: r primary_tool: ichorCNA measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools...Votes: 0GitHub stars: 6
- Liquid Biopsy Analytics Agent--> --- name: 'liquid-biopsy-analytics-agent' description: 'Comprehensive analysis of liquid biopsy data (ctDNA, CTCs) for cancer detection, MRD monitoring, and response tracking.' keywords: - liquid-biopsy - ctdna - mrd - cancer-detection - treatment-response measurable_outcome: 'Detects circulating tumor DNA with 0.01% sensitivity and accurately predicts treatment response in longitudinal samples.' allowed-tools: - read_file - run_shell_command --- The **Liquid Biopsy Analytics Agent** prov...Votes: 0GitHub stars: 6
- MRD EDGE Detection Agent--> --- name: 'mrd-edge-detection-agent' description: 'Ultra-sensitive AI-powered molecular residual disease detection using MRD-EDGE deep learning for sub-0.001% VAF ctDNA detection and early relapse prediction.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **MRD-EDGE Detection Agent** implements the MRD-EDGE (Enhanced Detection of ctDNA through Genomic Error suppression) deep learning algo...Votes: 0GitHub stars: 6
- OncologyConsultSurvivalLlm Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'oncology-consult-survival-llm' description: 'Guide zero-shot or fine-tuned LLM workflows for predicting cancer survival from initial oncology consultation documents with leakage control and cautious reporting.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- OncologyNeurosymbolicTrialMatching Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'oncology-neurosymbolic-trial-matching' description: 'Match oncology patients to clinical trials using knowledge-graph retrieval, symbolic eligibility reasoning, specialized agents, conflict resolution, and clinician-auditable evidence.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- Organoid Drug Response Agent--> --- name: 'organoid-drug-response-agent' description: 'AI-powered analysis of patient-derived organoid (PDO) drug screening for personalized oncology treatment selection and biomarker discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Organoid Drug Response Agent** provides AI-driven analysis of patient-derived organoid (PDO) drug screening data for personalized treatment selecti...Votes: 0GitHub stars: 6
- PDX Model Analysis Agent--> --- name: 'pdx-model-analysis-agent' description: 'AI-powered analysis of patient-derived xenograft (PDX) models for drug response prediction, translational research, and personalized treatment selection.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **PDX Model Analysis Agent** provides AI-driven analysis of patient-derived xenograft models for preclinical drug testing, translational re...Votes: 0GitHub stars: 6
- Pan Cancer MultiOmics Agent--> --- name: 'pan-cancer-multiomics-agent' description: 'AI-powered pan-cancer analysis integrating genomic, transcriptomic, proteomic, and epigenomic data for cancer subtyping, driver identification, and cross-cancer pattern discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Pan-Cancer Multi-Omics Agent** integrates multi-omics data across cancer types to identify shared oncogenic ...Votes: 0GitHub stars: 6
- Radiomics Pathomics Fusion Agent--> --- name: 'radiomics-pathomics-fusion-agent' description: 'AI-powered multimodal fusion of radiology (CT/MRI/PET) and pathology (H&E/IHC) imaging with clinical and genomic data for comprehensive cancer diagnostics and treatment prediction.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Radiomics Pathomics Fusion Agent** integrates multimodal medical imaging data from radiology (CT, MRI,...Votes: 0GitHub stars: 6
- RareNeoplasmRwdLlmExtraction Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'rare-neoplasm-rwd-llm-extraction' description: 'Extract registry-ready rare-neoplasm variables from clinical text using schema-first LLM workflows with temporal normalization, ontology mapping, provenance, adjudication, privacy, and validation.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- Tumor Clonal Evolution Agent--> --- name: 'tumor-clonal-evolution-agent' description: 'AI-powered analysis of tumor clonal architecture, subclonal dynamics, and evolutionary trajectories from multi-region sequencing and longitudinal liquid biopsy data.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Tumor Clonal Evolution Agent** analyzes intratumoral heterogeneity (ITH), reconstructs tumor phylogenies, and tracks clon...Votes: 0GitHub stars: 6
- Tumor Heterogeneity Agent--> --- name: 'tumor-heterogeneity-agent' description: 'AI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and longitudinal sequencing.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Tumor Heterogeneity Agent** provides comprehensive analysis of intratumor heterogeneity (ITH)...Votes: 0GitHub stars: 6
- Tumor Mutational Burden Agent--> --- name: 'tumor-mutational-burden-agent' description: 'Calculates and harmonizes Tumor Mutational Burden (TMB) across platforms to predict immunotherapy response.' keywords: - tmb - immunotherapy - biomarker - harmonization - oncology measurable_outcome: 'Harmonizes TMB scores across 5+ assay platforms with <5% variance from WES gold standard.' allowed-tools: - read_file - run_shell_command --- The **Tumor Mutational Burden Agent** provides comprehensive TMB analysis for immunotherapy re...Votes: 0GitHub stars: 6
- CtDNA Dynamics MRD Agent--> --- name: 'ctdna-dynamics-mrd-agent' description: 'AI-powered circulating tumor DNA dynamics analysis for molecular residual disease detection, treatment response monitoring, and early relapse prediction using liquid biopsy.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **ctDNA Dynamics MRD Agent** provides comprehensive analysis of circulating tumor DNA dynamics for molecular residual d...Votes: 0GitHub stars: 6
- Computational Pathology Agent--> --- name: computational-pathology-agent description: Analyze Whole Slide Images (WSI) for digital pathology, including tissue segmentation and feature extraction. keywords: - wsi - digital-pathology - deep-learning - resnet - openslide measurable_outcome: Preprocess and extract tissue patches from a 1GB+ .svs slide within 15 minutes for downstream ML tasks. license: MIT metadata: author: MD BABU MIA, PhD version: "1.0.0" compatibility: - system: python 3.9+ allowed-tools: - run_shell_comm...Votes: 0GitHub stars: 6
- DmmrCrcHistopathologyAgent Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'dmmr-crc-histopathology-agent' description: 'Predict dMMR risk in colorectal cancer histopathology workflows using tumor, non-tumor, and low-magnification WSI regions with validation handoff.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- Regulatory Affairs--> --- name: 'regulatory-drafter' description: 'Automates the drafting of regulatory documents (e.g., FDA CTD sections) with citation management and audit trails.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill assists regulatory affairs professionals by automatically generating sections of the Common Technical Document (CTD) from raw data and literature. It focuses on accuracy, tracea...Votes: 0GitHub stars: 6
- BioKernel--> --- name: biokernel description: AI Agentic Platform Core & MCP Server keywords: - kernel - os - mcp - api - system measurable_outcome: Routes 100% of API requests to correct sub-agent with <200ms latency. license: MIT metadata: author: AI Agentic Skills Team version: "1.0.0" compatibility: - system: Python 3.10+ allowed-tools: - run_shell_command - read_file --- The CoreKernel is the central orchestration layer of the AI Agentic Platform, managing context, routing tasks to specialized ag...Votes: 0GitHub stars: 6
- Meta Prompter--> --- name: meta-prompter description: Automatic prompt engineering & optimization keywords: - prompt-engineering - optimization - meta-prompting - llm - tuning measurable_outcome: Improves prompt performance metrics by >15% over baseline. license: MIT metadata: author: AI Agentic Skills Team version: "1.0.0" compatibility: - system: Python 3.10+ allowed-tools: - run_shell_command - read_file --- The Meta-Prompter is a tool for self-optimizing agent prompts. It analyzes agent performance an...Votes: 0GitHub stars: 6
- Ancestral Reconstruction--> --- name: bio-comparative-genomics-ancestral-reconstruction description: Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods. Infer ancient protein sequences and trace evolutionary trajectories through sequence history. Use when inferring ancestral states for protein resurrection or tracing evolutionary history. tool_type: mixed primary_tool: PAML measurable_outcome: Execute skill workflow successfully with valid output within 15 minute...Votes: 0GitHub stars: 6
- Hgt Detection--> --- name: bio-comparative-genomics-hgt-detection description: Detect horizontal gene transfer events using HGTector, compositional analysis, and phylogenetic incongruence methods. Identify foreign genes in bacterial and archaeal genomes from anomalous composition or unexpected phylogenetic placement. Use when searching for horizontally transferred genes or analyzing genome evolution in prokaryotes. tool_type: mixed primary_tool: HGTector measurable_outcome: Execute skill workflow successf...Votes: 0GitHub stars: 6
- Ortholog Inference--> --- name: bio-comparative-genomics-ortholog-inference description: Infer orthologous gene groups across species using OrthoFinder and ProteinOrtho. Identify orthologs, paralogs, and co-orthologs for comparative genomics and functional annotation transfer. Use when identifying gene orthologs across species or building orthogroups for evolutionary analysis. tool_type: cli primary_tool: OrthoFinder measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. a...Votes: 0GitHub stars: 6
- Positive Selection--> --- name: bio-comparative-genomics-positive-selection description: Detect positive selection using dN/dS (omega) tests with PAML codeml and HyPhy. Identify sites and branches under adaptive evolution through codon models and branch-site tests. Use when testing for adaptive evolution in gene families or identifying positively selected sites. tool_type: mixed primary_tool: PAML measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read...Votes: 0GitHub stars: 6
- Synteny Analysis--> --- name: bio-comparative-genomics-synteny-analysis description: Analyze genome collinearity and syntenic blocks using MCScanX, SyRI, and JCVI for comparative genomics. Detect conserved gene order, chromosomal rearrangements, and whole-genome duplications. Use when comparing genome structure between species or identifying conserved genomic regions. tool_type: mixed primary_tool: MCScanX measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-to...Votes: 0GitHub stars: 6
- Amr Surveillance--> --- name: bio-epidemiological-genomics-amr-surveillance description: Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs. tool_type: cli primary_tool: AMRFinderPlus measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - ...Votes: 0GitHub stars: 6
- Pathogen Typing--> --- name: bio-epidemiological-genomics-pathogen-typing description: Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates. tool_type: cli primary_tool: mlst measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_comma...Votes: 0GitHub stars: 6
- Phylodynamics--> --- name: bio-epidemiological-genomics-phylodynamics description: Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees. tool_type: python primary_tool: TreeTime measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowe...Votes: 0GitHub stars: 6
- Transmission Inference--> --- name: bio-epidemiological-genomics-transmission-inference description: Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders. tool_type: r primary_tool: TransPhylo measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allow...Votes: 0GitHub stars: 6
- Variant Surveillance--> --- name: bio-epidemiological-genomics-variant-surveillance description: Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern. tool_type: cli primary_tool: nextclade measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - ...Votes: 0GitHub stars: 6
- Distance Calculations--> --- name: bio-phylo-distance-calculations description: Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, or generating bootstrap consensus trees. tool_type: python primary_tool: Bio.Phylo.TreeConstruction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Compute dist...Votes: 0GitHub stars: 6
- Modern Tree Inference--> --- name: bio-phylo-modern-tree-inference description: Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-ng. Use when inferring publication-quality trees with model selection, ultrafast bootstrap, or partitioned analyses from sequence alignments. tool_type: cli primary_tool: IQ-TREE2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Build maximum likelihood phylogenetic trees w...Votes: 0GitHub stars: 6
- Tree Io--> --- name: bio-phylo-tree-io description: Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees. tool_type: python primary_tool: Bio.Phylo measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Parse, write, and convert phylogenetic tree files in various formats.Votes: 0GitHub stars: 6
- Tree Manipulation--> --- name: bio-phylo-tree-manipulation description: Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees. tool_type: python primary_tool: Bio.Phylo measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Modify phylogenetic tree structure: rooting, pruning, ladderizin...Votes: 0GitHub stars: 6
- Tree Visualization--> --- name: bio-phylo-tree-visualization description: Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib. Use when creating publication-quality tree figures, customizing colors and labels, or exporting to image formats. tool_type: python primary_tool: Bio.Phylo measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Draw phylogenetic trees using matplotlib integration.Votes: 0GitHub stars: 6
- Association Testing--> --- name: bio-population-genetics-association-testing description: Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests. tool_type: cli primary_tool: plink2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - r...Votes: 0GitHub stars: 6
- Linkage Disequilibrium--> --- name: bio-population-genetics-linkage-disequilibrium description: Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLINK, scikit-allel, and LDBlockShow. Use when calculating LD or pruning variants. tool_type: mixed primary_tool: plink2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_com...Votes: 0GitHub stars: 6
- Plink Basics--> --- name: bio-population-genetics-plink-basics description: PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC. tool_type: cli primary_tool: plink measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - ru...Votes: 0GitHub stars: 6
- Population Structure--> --- name: bio-population-genetics-population-structure description: Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic structure, and choose optimal K for admixture models. Use when analyzing population stratification with PCA or admixture. tool_type: cli primary_tool: plink2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-t...Votes: 0GitHub stars: 6
- Scikit Allel Analysis--> --- name: bio-population-genetics-scikit-allel-analysis description: Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structures. Use when analyzing population genetics in Python. tool_type: python primary_tool: scikit-allel measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read...Votes: 0GitHub stars: 6
- Selection Statistics--> --- name: bio-population-genetics-selection-statistics description: Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate population differentiation, test for departures from neutrality, and identify selective sweeps with scikit-allel and vcftools. Use when computing selection signatures like Fst or Tajima's D. tool_type: mixed primary_tool: scikit-allel measurable_outcome: Execute skill workflow successfully with valid output...Votes: 0GitHub stars: 6
- Multi Ancestry PRS Agent--> --- name: 'multi-ancestry-prs-agent' description: 'AI-powered multi-ancestry polygenic risk score calculation and optimization for equitable disease risk prediction across diverse global populations.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Multi-Ancestry PRS Agent** provides AI-optimized polygenic risk score calculation designed to work across diverse ancestral populations. It ad...Votes: 0GitHub stars: 6
- PRS Net Deep Learning Agent--> --- name: 'prs-net-deep-learning-agent' description: 'Geometric deep learning-based polygenic risk score prediction using PRS-Net for modeling gene interactions, enhanced disease prediction, and cross-ancestry portability.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **PRS-Net Deep Learning Agent** implements interpretable geometric deep learning for polygenic risk score prediction. PRS...Votes: 0GitHub stars: 6
- Pharmacogenomics Agent--> --- name: 'pharmacogenomics-agent' description: 'AI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.' keywords: - pharmacogenomics - precision-dosing - cpic-guidelines - adverse-events - multi-omics measurable_outcome: 'Provides validated dosing recommendations for >50 drugs with 99% concordance to CPIC guidelines.' allowed-tools: - read_file - run_shell_command --- The **Pharmacogenomics Agent** integrates AI and multi-omics data t...Votes: 0GitHub stars: 6
- Deep Visual Proteomics Agent--> --- name: 'deep-visual-proteomics-agent' description: 'AI-driven integration of cellular imaging, laser microdissection, and ultra-sensitive mass spectrometry for spatially-resolved single-cell proteomics.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Deep Visual Proteomics Agent** implements the Deep Visual Proteomics (DVP) workflow that combines AI-driven image analysis of cellular p...Votes: 0GitHub stars: 6
- Data Import--> --- name: bio-proteomics-data-import description: Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. Use when starting a proteomics analysis with raw or processed MS data. Handles contaminant filtering and missing value assessment. tool_type: mixed primary_tool: pyOpenMS measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_comman...Votes: 0GitHub stars: 6
- Dia Analysis--> --- name: bio-proteomics-dia-analysis description: Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling. tool_type: cli primary_tool: diann measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Differential Abundance--> --- name: bio-proteomics-differential-abundance description: Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups. tool_type: mixed primary_tool: MSstats measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Peptide Identification--> --- name: bio-proteomics-peptide-identification description: Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches. tool_type: mixed primary_tool: pyOpenMS measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6