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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documentation scientific computing AI 技能
发现 documentation scientific computing 相关 Skills，比较来源仓库和用途，查看适合你工作流的技能说明。
分类目录: documentation scientific computing
documentation scientific computing 清除筛选
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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
geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
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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
research-lookup
Multi-provider research lookup supporting Gemini Deep Research (60-min comprehensive analysis) and Perplexity Sonar (fast web-grounded research). Intelligently routes between providers based on research mode an...
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GitHub
research-patterns
Research methodology and best practices for finding existing patterns
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GitHub
power-analysis
Calculate statistical power and required sample sizes for research studies. Use when: (1) Designing experiments to determine sample size, (2) Justifying sample size for grant proposals or protocols, (3) Evaluat...
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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
recursion
Recursive algorithms and divide-and-conquer strategies
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GitHub
strings
String algorithms and pattern matching techniques
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GitHub
golden-dataset-curation
Quality criteria, workflows, and multi-agent analysis patterns for curating high-quality golden dataset entries
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GitHub
researcher
Researches topics in-depth and generates comprehensive summaries and references. Use when trying to deeply understand a topic or use a new framework.
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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
hic-normalization
Automatically detect and normalize Hi-C data. Only .cool or .mcool file is supported. All .mcool files are then checked for existing normalization (supports bins/weight only) and balanced if none of the normali...
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GitHub
genomic-feature-annotation
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions...
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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
alignment-level-qc
Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read gro...
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GitHub
nested-tad-detection
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and re...
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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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默认按已收录数据中的 GitHub 仓库 Stars 排序。Stars 属于来源仓库，同一仓库的多个技能可能共享相同数值；它反映仓库关注度，不代表单个技能的安装量或质量评分。