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evaluation-v2
Anthropic-aligned medical safety evaluation with pass^k metrics, failure taxonomy, and anti-gaming graders
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tools computational chemistry AI Skills
Discover tools computational chemistry skills, compare source repositories and read the instructions for each workflow.
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hol4
HOL4 proof development pipeline - planning, sketching, and proving phases. (project)
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GitHub
atomic-thought
INVOKE for research tasks and multi-source understanding. Produces visible dependency graphs and contracted answers. Use during research phase of workflow. Triggers: researching topics, gathering information be...
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GitHub
functional-enrichment
Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform G...
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GitHub
motif-scanning
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined...
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GitHub
local-methylation-profile
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CT...
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GitHub
loop-annotation
This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.
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GitHub
peak-calling
Perform peak calling for ChIP-seq or ATAC-seq data using MACS3, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
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GitHub
hic-compartments-calling
This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools, cooltools-tools, and plot-hic-tools servers.
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GitHub
atacseq-qc
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use thi...
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GitHub
chipseq-qc
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks...
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GitHub
regulatory-community-analysis-chia-pet
This skill performs protein-mediated regulatory community analysis from ChIA-PET datasets and provide a way for visualizing the communities. Use this skill when you have a annotated peak file (in BED format) fr...
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GitHub
hic-compartment-shift
This skill performs A/B compartment shift analysis between two Hi-C samples.
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GitHub
zero-day-hunting-methodology
Systematic approach to discovering novel vulnerabilities through code analysis, fuzzing, and attack surface research
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GitHub
exploit-development-workflow
Systematic methodology for developing reliable exploits from vulnerability discovery to weaponization
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GitHub
ship-dynamics-6dof
6DOF ship dynamics, equations of motion, seakeeping analysis, and natural frequency calculations
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GitHub
hydrodynamic-analysis
Hydrodynamic analysis using BEM, RAOs, added mass, damping, and wave loads for offshore structures
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GitHub
trend-modeling
This skill should be used when the user asks to "model trends with limited data", "three-valued logic analysis", "scenario generation", "transitional graphs", "qualitative trend analysis", "uncertain data analy...
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GitHub
regulatory-review
This skill should be used when the user asks to "analyze regulations", "regulatory landscape", "compliance requirements", "legal considerations", "regulatory risk", "industry regulations", "compliance analysis"...
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GitHub
sdd-state-management
SDD state tracking - phases, gates, lanes, and state.md structure
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GitHub
medcom
Invoke MEDCOM for military medical advisory, ACGME interpretation, and domain expertise. Advisory-only agent that surfaces clinical information for physician decision-making. Never makes medical decisions.
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GitHub
acgme-compliance
ACGME regulatory compliance expertise for medical residency scheduling. Use when validating schedules, checking work hour limits, supervision ratios, or answering compliance questions. Integrates with MCP valid...
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GitHub
compliance-validation
ACGME & institutional rule checking with systematic audit workflows, historical analysis, and violation remediation. Use for compliance audits, violation investigation, and regulatory reporting.
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GitHub
tamc-cpsat-constraints
CP-SAT constraint model for TAMC Family Medicine scheduling optimization. Use when building or debugging the OR-Tools solver for faculty/resident scheduling. Documents hard constraints, soft constraints, decisi...
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The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.