GitHub
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use...
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business computational chemistry AI Skills
Discover business computational chemistry skills, compare source repositories and read the instructions for each workflow.
Categories: business computational chemistry
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GitHub
rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, pro...
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GitHub
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommenda...
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GitHub
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
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GitHub
alphafold-database
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
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GitHub
prisma-diagram
Generate PRISMA 2020 flow diagrams for systematic reviews. Use when: (1) Conducting systematic literature reviews, (2) Documenting screening process, (3) Reporting study selection for publications, (4) Demonstr...
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GitHub
structured-analytic-techniques
Guide cyber threat intelligence analysts through the Diamond Model framework and Structured Analytic Techniques (SATs) from Heuer. Use when analysts need help with: (1) Organizing attack data using the Diamond...
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GitHub
evaluation-v2
Anthropic-aligned medical safety evaluation with pass^k metrics, failure taxonomy, and anti-gaming graders
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GitHub
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
analyzing-research-documents
Extracts high-value insights from research documents, RCAs, design docs, and memos - filters aggressively to return only actionable information. Research equivalent of analyzing-implementations skill.
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GitHub
ship-dynamics-6dof
6DOF ship dynamics, equations of motion, seakeeping analysis, and natural frequency calculations
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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.