数据与复现

aeon

aeon：Aeon是一个兼容 scikit-learn Python 工具包 ，用于 时序机器学习。 It provides state-of- -art algorithms ，用于 分类，回归，聚类，预测，异常检测，分割，、 相似性检索…

agent-browser

agent-browser：Browse web ，用于 any task — research topics，read articles，interact ，支持 web apps，fill forms，take screenshots，…

arxiv-database

arxiv-database：This skill provides Python tools ，用于 searching 、 retrieving preprints ，面向 arXiv.org ，通过 its public Atom A…

Astropy

Astropy是一个core Python package ，用于 astronomy，providing essential functionality ，用于 astronomical research 、 数据分析。 Use astr…

bayesian-optimizer

bayesian-optimizer：Bayesian optimization ，用于 experimental design 、 hyperparameter tuning in biomedical research。

Benchling Integration

Benchling Integration：Benchling是一个cloud 平台 ，用于 life sciences R&D。 访问 registry entities (DNA，proteins)，inventory，electron…

bgpt-paper-search

bgpt-paper-search：BGPT是一个remote MCP server that searches curated database of scientific papers built ，面向 raw experimenta…

bio-alignment-files-bam-statistics

bio-alignment-files-bam-statistics：Compute alignment statistics：flagstat，idxstats，coverage depth。

bio-alignment-msa-statistics

bio-alignment-msa-statistics：Calculate alignment statistics ，涵盖 sequence identity，conservation scores，substitution matri…

bio-blast-searches

bio-blast-searches：运行 BLAST searches against local 或 remote databases ，用于 sequence homology。

bio-causal-genomics-colocalization-analysis

bio-causal-genomics-colocalization-analysis：Colocali。

bio-causal-genomics-fine-mapping

bio-causal-genomics-fine-mapping：Fine-mapping narrows GWAS association signals to identify likely causal variants。 Key o…

bio-causal-genomics-mediation-analysis

bio-causal-genomics-mediation-analysis：Decompose genetic effects into direct 、 indirect paths through mediating variable…

bio-causal-genomics-mendelian-randomization

bio-causal-genomics-mendelian-randomization：Estimate causal effects between exposures 、 outcomes ，使用 genetic variants as…

bio-causal-genomics-pleiotropy-detection

bio-causal-genomics-pleiotropy-detection：Hori。

bio-chipseq-differential-binding

bio-chipseq-differential-binding：Differential binding analysis ，使用 DiffBind。 比较 ChIP-seq peaks between conditions ，支持 st…

bio-chipseq-peak-annotation

bio-chipseq-peak-annotation：Annotate ChIP-seq peaks to genomic features 、 genes ，使用 ChIPseeker。 Assign peaks to promoter…

bio-chipseq-visualization

bio-chipseq-visualization：可视化 ChIP-seq data ，使用 deepTools，Gviz，、 ChIPseeker。 创建 heatmaps，profile plots，、 genome browser…

bio-clinical-databases-polygenic-risk

bio-clinical-databases-polygenic-risk：Calculate polygenic risk scores ，使用 PRSice-2，LDpred2，或 PRS-CS ，面向 GWAS summary sta…

bio-consensus-sequences

bio-consensus-sequences：生成 consensus FASTA sequences by applying VCF variants to reference ，使用 bcftools consensus。 适合在cr…

bio-copy-number-cnv-visualization

bio-copy-number-cnv-visualization：可视化 copy number profiles，segments，、 compare across samples。 创建 publication-quality plo…

bio-crispr-screens-base-editing-analysis

bio-crispr-screens-base-editing-analysis：分析 base editing 、 prime editing outcomes ，涵盖 editing efficiency，bystander edits…

bio-crispr-screens-batch-correction

bio-crispr-screens-batch-correction：Batch effect correction ，用于 CRISPR screens。 Covers normalization across batches，tech…

bio-crispr-screens-crispresso-editing

bio-crispr-screens-crispresso-editing：CRISPResso2 ，用于 analyzing CRISPR gene editing outcomes。 Quantifies indels，HDR effi…

bio-crispr-screens-hit-calling

bio-crispr-screens-hit-calling：Statistical methods ，用于 calling hits in CRISPR screens。 Covers MAGeCK，BAGEL2，drugZ，、 cust…

bio-crispr-screens-jacks-analysis

bio-crispr-screens-jacks-analysis：JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) ，用于 modeling sgRNA efficacy 、 g…

bio-crispr-screens-library-design

bio-crispr-screens-library-design：CRISPR 库 design ，用于 genetic screens。 Covers sgRNA selection，库 composition，control desi…

bio-crispr-screens-mageck-analysis

bio-crispr-screens-mageck-analysis：MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) ，用于 pooled CRISPR s…

bio-crispr-screens-screen-qc

bio-crispr-screens-screen-qc：Quality control ，用于 pooled CRISPR screens。 Covers 库 representation，read distribution，replic…

bio-data-visualization-circos-plots

bio-data-visualization-circos-plots：Circular genome visualization ，支持 Circos 或 pycirclize。

bio-data-visualization-genome-tracks

bio-data-visualization-genome-tracks：Multi-panel genome track plots ，支持 pyGenomeTracks。

bio-data-visualization-ggplot2-fundamentals

bio-data-visualization-ggplot2-fundamentals：R ggplot2 ，用于 publication-quality genomics 、 omics figures。

bio-data-visualization-heatmaps-clustering

bio-data-visualization-heatmaps-clustering：Hierarchical 聚类 heatmaps ，支持 ComplexHeatmap 或 seaborn。

bio-data-visualization-interactive-visualization

bio-data-visualization-interactive-visualization：Interactive omics visualizations ，支持 Plotly，Bokeh，或 shiny。

bio-data-visualization-multipanel-figures

bio-data-visualization-multipanel-figures：Compose multipanel publication figures ，支持 cowplot 或 patchwork。

bio-data-visualization-specialized-omics-plots

bio-data-visualization-specialized-omics-plots：Specialized plots：lollipop (mutations)，circomap，oncoprint。

bio-data-visualization-upset-plots

bio-data-visualization-upset-plots：UpSet plots ，用于 multi-set intersection visualization。

bio-data-visualization-volcano-customization

bio-data-visualization-volcano-customization：Customized volcano plots ，支持 ggplot2 或 matplotlib ，用于 DE results。

bio-de-edger-basics

bio-de-edger-basics：执行 differential expression analysis ，使用 edgeR in R/Bioconductor。 可用于analyzing RNA-seq count data ，支持…

bio-de-visualization

bio-de-visualization：可视化 differential expression results ，使用 DESeq2/edgeR built-in functions。 Covers plotMA，plotDispEsts…

bio-entrez-link

bio-entrez-link：获取 linked records across NCBI Entrez databases。

bio-epidemiological-genomics-amr-surveillance

bio-epidemiological-genomics-amr-surveillance：检测 、 track antimicrobial resistance genes ，使用 AMRFinderPlus 、 ResFinder ，支…

bio-epidemiological-genomics-pathogen-typing

bio-epidemiological-genomics-pathogen-typing：执行 multi-locus sequence typing (MLST)，core genome MLST，、 SNP-based strain t…

bio-epidemiological-genomics-phylodynamics

bio-epidemiological-genomics-phylodynamics：Construct time-scaled phylogenies 、 infer evolutionary dynamics ，使用 TreeTime…

bio-epidemiological-genomics-transmission-inference

bio-epidemiological-genomics-transmission-inference：推断 pathogen transmission networks 、 identify likely transmission pai…

bio-epidemiological-genomics-variant-surveillance

bio-epidemiological-genomics-variant-surveillance：Assign pathogen lineages 、 track variants ，使用 Nextclade 、 pangolin ，用于…

bio-epitranscriptomics-modification-visualization

bio-epitranscriptomics-modification-visualization：可视化 RNA modification profiles 、 metagene plots。

bio-experimental-design-power-analysis

bio-experimental-design-power-analysis：Statistical power analysis ，用于 detecting differential signals。

bio-flow-cytometry-differential-analysis

bio-flow-cytometry-differential-analysis：Differential abundance 、 state analysis ，用于 cytometry data。 比较 cell populations…

bio-gatk-variant-calling

bio-gatk-variant-calling：Variant calling ，支持 GATK HaplotypeCaller following best practices。 Covers germline SNP/indel ca…

bio-genome-engineering-base-editing-design

bio-genome-engineering-base-editing-design：Design guides ，用于 cytosine 、 adenine base editing ，使用 editing window optimiza…

bio-genome-engineering-grna-design

bio-genome-engineering-grna-design：Design guide RNAs ，用于 CRISPR-Cas9/Cas12a experiments ，使用 CRISPRscan 、 local scoring a…

bio-genome-engineering-hdr-template-design

bio-genome-engineering-hdr-template-design：Design homology-directed repair donor templates ，用于 CRISPR knock-ins ，使用 prim…

bio-genome-engineering-off-target-prediction

bio-genome-engineering-off-target-prediction：预测 CRISPR off-target sites ，使用 Cas-OFFinder 、 CFD scoring algorithms。 Ident…

bio-genome-engineering-prime-editing-design

bio-genome-engineering-prime-editing-design：Design pegRNAs ，用于 prime editing ，使用 PrimeDesign algorithms。 生成 spacer，PBS，、…

bio-hi-c-analysis-contact-pairs

bio-hi-c-analysis-contact-pairs：Process Hi-C read pairs ，使用 pairtools。 解析 alignments，filter duplicates，classify pairs，、…

bio-hi-c-analysis-hic-differential

bio-hi-c-analysis-hic-differential：比较 Hi-C contact matrices between conditions to identify differential chromatin intera…

bio-hi-c-analysis-hic-visualization

bio-hi-c-analysis-hic-visualization：可视化 Hi-C contact matrices，TADs，loops，、 genomic features ，使用 matplotlib，cooltools，、 H…

bio-imaging-mass-cytometry-spatial-analysis

bio-imaging-mass-cytometry-spatial-analysis：Spatial analysis of cell neighborhoods 、 interactions in IMC data。 Covers ne…

bio-local-blast

bio-local-blast：Set up 、 run BLAST+ locally ，支持 custom databases。

bio-longread-qc

bio-longread-qc：Quality control ，用于 long-read sequencing data ，使用 NanoPlot，NanoStat，、 chopper。 生成 QC reports，filter read…

bio-metabolomics-normalization-qc

bio-metabolomics-normalization-qc：Quality control 、 normalization ，用于 metabolomics data。 Covers QC-based correction，batc…

bio-metabolomics-statistical-analysis

bio-metabolomics-statistical-analysis：统计分析 ，用于 metabolomics data。 Covers univariate testing，multivariate methods (PCA，PL…

bio-metagenomics-kraken

bio-metagenomics-kraken：Taxonomic 分类 of metagenomic reads ，使用 Kraken2。 Fast k-mer based 分类 against RefSeq database。 适合在p…

bio-metagenomics-visualization

bio-metagenomics-visualization：可视化 metagenomic profiles ，使用 R (phyloseq，microbiome) 、 Python (matplotlib，seaborn)。 创建 st…

bio-methylation-methylkit

bio-methylation-methylkit：DNA methylation analysis ，支持 methylKit in R。 Import Bismark coverage files，filter by coverage，…

bio-pathway-enrichment-visualization

bio-pathway-enrichment-visualization：可视化 enrichment results ，使用 enrichplot package functions。 Covers dotplot，barplot，cne…

bio-pathway-go-enrichment

bio-pathway-go-enrichment：Gene Ontology over-representation analysis ，使用 clusterProfiler enrichGO。 支持 all three ontologi…

bio-pathway-kegg-pathways

bio-pathway-kegg-pathways：KEGG pathway 、 module enrichment analysis ，使用 clusterProfiler enrichKEGG 、 enrichMKEGG。 支持 400…

bio-pathway-reactome

bio-pathway-reactome：Reactome pathway enrichment ，使用 ReactomePA package。 执行 over-representation analysis 、 GSEA ，支持 visu…

bio-population-genetics-scikit-allel-analysis

bio-population-genetics-scikit-allel-analysis：Population genetics analysis ，支持 scikit-allel：diversity，Fst，haplotypes。

bio-proteomics-differential-abundance

bio-proteomics-differential-abundance：统计检验 ，用于 differentially abundant proteins between conditions。 Covers limma 、 MSsta…

bio-reporting-figure-export

bio-reporting-figure-export：Export 论文级图表 in PDF/SVG/TIFF at specified DPI。

bio-reporting-rmarkdown-reports

bio-reporting-rmarkdown-reports：Render Rmarkdown reports ，支持 integrated plots 、 statistics。

bio-sashimi-plots

bio-sashimi-plots：创建 sashimi plots showing RNA-seq read coverage 、 splice junction counts ，使用 ggsashimi 或 rmats2sashimip…

bio-sequence-statistics

bio-sequence-statistics：Calculate sequence statistics (N50，length distribution，GC content，summary reports) ，使用 Biopython…

bio-single-cell-cell-communication

bio-single-cell-cell-communication：推断 cell-cell communication networks ，面向 scRNA-seq data ，使用 CellChat，NicheNet，、 LIANA…

bio-single-cell-metabolite-communication

bio-single-cell-metabolite-communication：分析 metabolite-mediated cell-cell communication ，使用 MeboCost ，用于 metabolic signa…

bio-spatial-transcriptomics-spatial-communication

bio-spatial-transcriptomics-spatial-communication：分析 cell-cell communication in spatial transcriptomics data ，使用 ligand-…

bio-spatial-transcriptomics-spatial-statistics

bio-spatial-transcriptomics-spatial-statistics：Compute spatial statistics ，用于 spatial transcriptomics data ，使用 Squidpy。…

bio-spatial-transcriptomics-spatial-visualization

bio-spatial-transcriptomics-spatial-visualization：可视化 spatial transcriptomics data ，使用 Squidpy 、 Scanpy。 创建 tissue plots…

bio-tcr-bcr-analysis-repertoire-visualization

bio-tcr-bcr-analysis-repertoire-visualization：创建 publication-quality visualizations of immune repertoire data ，涵盖 circos…

bio-vcf-statistics

bio-vcf-statistics：生成 variant statistics，sample concordance，、 quality metrics ，使用 bcftools stats 、 gtcheck。 适合在evaluatin…

bio-workflows-crispr-screen-pipeline

bio-workflows-crispr-screen-pipeline：CRISPR screen：guide counting → MAGeCK → hit calling → visualization。

bio-workflows-expression-to-pathways

bio-workflows-expression-to-pathways：End-to-end workflow ，面向 differential expression to GO/KEGG/Reactome enrichment 、 pa…

bio-workflows-imc-pipeline

bio-workflows-imc-pipeline：Imaging mass cytometry：分割 → phenotyping → spatial analysis。

bio-workflows-metabolic-modeling-pipeline

bio-workflows-metabolic-modeling-pipeline：Metabolic model reconstruction → FBA → 模拟 → visualization。

bio-workflows-metabolomics-pipeline

bio-workflows-metabolomics-pipeline：LC-MS/GC-MS：preprocessing → annotation → 统计分析。

bioinformatics-singlecell

bioinformatics-singlecell：General single-cell bioinformatics：聚类，trajectory，cell communication。

biomedical-data-analysis

biomedical-data-analysis：Comprehensive biomedical 数据分析：statistics，visualization，、 interpretation。

BioServices

BioServices是一个Python package providing programmatic access to approximately 40 bioinformatics web services 、 databases。…

bulk-rna-seq-deseq2-analysis-with-omicverse

bulk-rna-seq-deseq2-analysis-with-omicverse：Use this skill when user wants to reproduce DESeq2 workflow showcased in [`t…

bulk-rna-seq-differential-expression-with-omicverse

bulk-rna-seq-differential-expression-with-omicverse：Follow this skill to run end-to-end differential expression (DEG) wo…

care-coordination

care-coordination：Care coordination agent：multi-disciplinary team communication 、 care plan management。

Citation Management

Citation Management：管理 citations systematically throughout research 、 writing process。 This skill provides tools 、 strat…

Clinical Decision Support

Clinical Decision Support：生成 professional clinical decision support (CDS) documents ，用于 pharmaceutical companies，clinica…

Clinical Reports

Clinical Reports：Clinical report writing是一个process of documenting medical information ，支持 precision，accuracy，、 complianc…

clinicaltrials-database

clinicaltrials-database：ClinicalTrials.gov是一个comprehensive registry of clinical studies conducted worldwide，maintained b…

convergence-study

convergence-study：Spatial 、 temporal convergence analysis ，支持 Richardson extrapolation 、 Grid Convergence Index (GCI) ，用…

Dask

Dask是一个Python 库 ，用于 parallel 、 distributed computing that enables three critical capabilities：- **Larger-than-memory exe…

Data Commons

Data Commons：Use `idc-index` Python package to query 、 download public cancer imaging data ，面向 National Cancer Institute…

data-stats-analysis

data-stats-analysis：This skill enables you to perform rigorous statistical analyses ，涵盖 t-tests，ANOVA，correlation analys…

data-transform

data-transform：This skill enables you to perform comprehensive data transformations ，涵盖 cleaning，normali。

data-visualization-biomedical

data-visualization-biomedical：Biomedical-specific data visualization：clinical trial plots，survival curves，forest plots。

data-visualization-expert

data-visualization-expert：Expert data visualization ，用于 complex scientific 、 clinical 数据集s。

data-viz-plots

data-viz-plots：This skill enables you to create professional scientific visuali。

datacommons-client

datacommons-client：提供 comprehensive access to Data Commons Python API v2 ，用于 querying statistical observations，exploring…

deepTools

deepTools是一个comprehensive suite of Python command-line tools designed ，用于 processing 、 analy。

Denario

Denario是一个multiagent AI system designed to automate scientific 科研工作流 ，面向 initial 数据分析 through publication-ready manuscri…

dhdna-profiler

dhdna-profiler：structured system ，用于 extracting cognitive fingerprint of any text's author。 Based on Digital Human DNA (…

differentiation-schemes

differentiation-schemes：Select 、 apply numerical differentiation schemes ，用于 PDE/ODE discretization。 适合在choosing finite…

DNAnexus Integration

DNAnexus Integration：DNAnexus是一个cloud 平台 ，用于 biomedical 数据分析 、 genomics。 构建 、 deploy apps/applets，manage data objects，ru…

docx

docx：.docx file is。

equity-scorer

equity-scorer：Compute HEIM diversity 、 equity metrics ，面向 VCF 或 ancestry data。 生成 heterozygosity，FST，PCA plots，、 composi…

etetoolkit

etetoolkit：ETE (Environment ，用于 Tree Exploration) is 工具包 ，用于 phylogenetic 、 hierarchical tree analysis。 Manipulate trees…

Exploratory Data Analysis

Exploratory Data Analysis：执行 comprehensive exploratory 数据分析 (EDA) on scientific data files across multiple domains。 This…

find-skills

find-skills：帮助 users discover 、 install agent skills when they ask questions like "how do I do X"，"find skill ，用于 X"，"is…

FluidSim

FluidSim是一个object-oriented Python 框架 ，用于 high-performance computational fluid dynamics (CFD) 模拟s。 It provides solvers ，用…

FRED Economic Data

FRED Economic Data：访问 comprehensive 经济数据 through FRED (Federal Reserve 经济数据)，database maintained by Federal Reserve Bank…

Generate Image

Generate Image：生成 、 edit high-quality images ，使用 OpenRouter's image generation models ，涵盖 FLUX.2 Pro 、 Gemini 3.1 Flash…

geomaster

geomaster：Comprehensive 地理空间 science skill covering GIS，遥感，spatial analysis，、 ML ，用于 Earth observation across 70+ topics…

GeoPandas

GeoPandas extends pandas to enable spatial operations on geometric types。 It combines capabilities of pandas 、 shapely ，…

gnomad-database

gnomad-database：Genome Aggregation Database (gnomAD) is largest publicly available collection of human genetic variation…

gtex-database

gtex-database：Genotype-Tissue Expression (GTEx) project provides comprehensive resource ，用于 studying tissue-specific gen…

gwas-database

gwas-database：The GWAS Catalog是一个comprehensive repository of published genome-wide association studies maintained by Nat…

hedgefundmonitor

hedgefundmonitor：Free，open REST API ，面向 U.S。 Office of Financial Research (OFR) providing aggregated hedge fund time ser…

HypoGeniC

HypoGeniC：Hypogenic provides automated hypothesis generation 、 testing ，使用 large language models to accelerate scientifi…

infographics

infographics：Infographics are visual representations of information，data，或 knowledge designed to present complex content…

instrument-data-to-allotrope

instrument-data-to-allotrope：Convert laboratory instrument output files (PDF，CSV，Excel，TXT) to Allotrope Simple Model (A…

KEGG

KEGG (Kyoto Encyclopedia of Genes 、 Genomes) is comprehensive bioinformatics resource ，用于 biological pathway analysis 、…

labarchive-integration

labarchive-integration：LabArchives是一个electronic lab notebook 平台 ，用于 research documentation 、 data management。 访问 noteboo…

LaminDB

LaminDB是一个open-source data 框架 ，用于 biology designed to make data queryable，traceable，reproducible，、 FAIR (Findable，Access…

LatchBio Integration

LatchBio Integration：Latch是一个Python 框架 ，用于 building 、 deploying bioinformatics workflows as serverless pipelines。 Built…

LaTeX Posters

LaTeX Posters：Research posters are critical medium ，用于 scientific communication at conferences，symposia，、 academic event…

linear-solvers

linear-solvers：Select 、 configure linear solvers ，用于 systems Ax=b in dense 、 sparse problems。 适合在choosing direct vs iter…

lobster-bioinformatics

lobster-bioinformatics：运行 bioinformatics analyses ，使用 Lobster AI - single-cell RNA-seq，bulk RNA-seq，literature mining，数据…

markdown-mermaid-writing

markdown-mermaid-writing：This skill teaches you — 、 enforces standard ，用于 — creating scientific documentation ，使用 **mark…

Market Research Reports

Market Research Reports：Market research reports are comprehensive strategic documents that analy。

matlab

matlab：MATLAB是一个numerical computing environment optimized ，用于 matrix operations 、 scientific computing。 GNU Octave是一个fre…

Matplotlib

Matplotlib is Python's foundational visuali。

monarch-database

monarch-database：Monarch Initiative (https：//monarchinitiative.org/) is multi-species integrated knowledgebase that link…

multi-search-engine

multi-search-engine：Multi search engine integration ，支持 17 engines (8 CN + 9 Global)。 支持 advanced search operators，time…

NetworkX

NetworkX是一个Python package ，用于 creating，manipulating，、 analy。

nonlinear-solvers

nonlinear-solvers：Select 、 configure nonlinear solvers ，用于 f(x)=0 或 min F(x)。 可用于Newton methods，quasi-Newton (BFGS，L-BFG…

numerical-integration

numerical-integration：Select 、 configure time integration methods ，用于 ODE/PDE 模拟s。 适合在choosing explicit/implicit schemes…

numerical-stability

numerical-stability：分析 、 enforce numerical stability ，用于 time-dependent PDE 模拟s。 适合在selecting time steps，choosing explic…

ontology-explorer

ontology-explorer：解析，navigate，、 query 材料科学 ontology structure (classes，properties，hierarchy)。 支持 OWL/XML format ，面向 OCDO…

ontology-mapper

ontology-mapper：映射 材料科学 terms，crystal structures，、 sample descriptions to ontology classes 、 properties。 支持 any ontology…

ontology-validator

ontology-validator：Validate material sample annotations 、 data structures against ontology constraints。 Catches unknown…

OpenAlex

OpenAlex是一个comprehensive open catalog of 240M+ scholarly works，authors，institutions，topics，sources，publishers，、 funders。…

Opentrons Integration

Opentrons Integration：Opentrons是一个Python-based 实验室自动化 平台 ，用于 Flex 、 OT-2 robots。 撰写 Protocol API v2 protocols ，用于 liquid…

opentrons-protocol-agent

opentrons-protocol-agent：Opentrons liquid handler protocol design ，用于 automated lab workflows。

Paper-2-Web

Paper-2-Web：This skill enables transformation of academic papers into multiple promotional 、 presentation formats ，使用 Pa…

parameter-optimization

parameter-optimization：Explore 、 optimize 模拟 parameters ，通过 design of experiments (DOE)，sensitivity analysis，、 optimizer…

pdf

pdf：This guide covers essential PDF processing operations ，使用 Python libraries 、 command-line tools。 用于 advanced feature…

Peer Review

Peer Review：Peer review是一个systematic process ，用于 evaluating scientific manuscripts。 Assess methodology，statistics，design…

performance-profiling

performance-profiling：Identify computational bottlenecks，analyze scaling behavior，estimate memory requirements，、 receive…

Perplexity Search

Perplexity Search：执行 AI-powered web searches ，使用 Perplexity models through LiteLLM 、 OpenRouter。 Perplexity provides rea…

Plotly

Plotly：Python graphing 库 ，用于 creating interactive，publication-quality visualizations ，支持 40+ chart types。

Polars

Polars是一个lightning-fast DataFrame 库 ，用于 Python 、 Rust built on Apache Arrow。 Work ，支持 Polars' expression-based API，la。

Polars

Polars：polars-bio是一个high-performance Python 库 ，用于 genomic interval operations 、 bioinformatics file I/O，built on Polars，…

post-processing

post-processing：提取，analyze，、 visualize 模拟 output data。 可用于field extraction，时序分析，line profiles，statistical summaries，deri…

pptx

pptx：| Task | Guide | |------|-------| | Read/analyze content | `python -m markitdown presentation.pptx` | | Edit 或 crea…

PPTX Posters

PPTX Posters：**⚠️ USE THIS SKILL ONLY WHEN USER EXPLICITLY REQUESTS PPTX/POWERPOINT POSTER FORMAT.** ，用于 standard resear…

protocolsio-integration

protocolsio-integration：Protocols.io是一个comprehensive 平台 ，用于 developing，sharing，、 managing scientific protocols。 This ski…

pubmed-search

pubmed-search：检索 PubMed ，用于 scientific literature。 Triggers on "pubmed"，"papers"，"literature"，"publications"，"research o…

PyDESeq2

PyDESeq2是一个Python implementation of DESeq2 ，用于 differential expression analysis ，支持 bulk RNA-seq data。 Design 、 execute…

pydicom

pydicom：Pydicom是一个pure Python package ，用于 working ，支持 DICOM files，standard format ，用于 medical imaging data。 This skill p…

PyLabRobot

PyLabRobot是一个hardware-agnostic，pure Python Software Development Kit ，用于 automated 、 autonomous laboratories。 Use this sk…

Pymatgen

Pymatgen是一个comprehensive Python 库 ，用于 materials analysis that powers Materials Project。 创建，analy。

PyMC

PyMC是一个Python 库 ，用于 Bayesian modeling 、 probabilistic programming。 构建，fit，validate，、 compare Bayesian models ，使用 PyMC's…

PyTorch Lightning

PyTorch Lightning是一个深度学习 框架 that organi。

pyzotero

pyzotero：Pyzotero是一个Python wrapper ，用于 [Zotero API v3](https：//www.zotero.org/support/dev/web_api/v3/start)。 Use it to p…

Reactome

Reactome是一个free，open-source，curated pathway database ，支持 2，825+ human pathways。 Query biological pathways，perform overre…

Research Grants

Research Grants：Research grant writing是一个process of developing competitive funding proposals ，用于 federal agencies 、 foun…

Research Lookup

Research Lookup：This skill provides real-time research information lookup ，支持 **intelligent backend routing**：- **Parall…

Scanpy

Scanpy是一个scalable Python 工具包 ，用于 analy。

Scholar Evaluation

Scholar Evaluation：Apply ScholarEval 框架 to systematically evaluate scholarly 、 research work。 This skill provides struct…

Scientific Critical Thinking

Scientific Critical Thinking：Critical thinking是一个systematic process ，用于 evaluating scientific rigor。 Assess methodology，…

Scientific Schematics

Scientific Schematics：Scientific schematics 、 diagrams transform complex concepts into clear visual representations ，用于…

Scientific Slides

Scientific Slides：Scientific presentations are critical medium ，用于 communicating research，sharing findings，、 engaging ，支…

Scientific Visualization

Scientific Visualization：Scientific visuali。

Scientific Writing

Scientific Writing：**This is core skill ，用于 deep research 、 writing tool**—combining AI-driven deep research ，支持 well-fo…

scikit-bio

scikit-bio是一个comprehensive Python 库 ，用于 working ，支持 biological data。 Apply this skill ，用于 bioinformatics analyses spanni…

Seaborn

Seaborn是一个Python visuali。

SHAP

SHAP是一个unified approach to explain 机器学习 model outputs ，使用 Shapley values ，面向 cooperative game theory。 This skill provide…

SimPy

SimPy是一个process-based discrete-event 模拟 框架 based on standard Python。 Use SimPy to model systems where entities (customer…

simulation-orchestrator

simulation-orchestrator：Orchestrate multi-模拟 campaigns ，涵盖 parameter sweeps，batch jobs，、 result aggregation。 可用于running…

simulation-validator

simulation-validator：Validate 模拟s before，during，、 after execution。 可用于pre-flight checks，runtime monitoring，post-run vali…

single-cell-cellphonedb-communication-mapping

single-cell-cellphonedb-communication-mapping：Apply this skill when user wants to quantify ligand–receptor communication…

single-cell-rna-qc

single-cell-rna-qc：执行 quality control on single-cell RNA-seq data (.h5ad 或.h5 files) ，使用 scverse best practices ，支持 MAD-…

spatial-communication

spatial-communication。

spatial-statistics

spatial-statistics。

spatial-transcriptomics-tutorials-with-omicverse

spatial-transcriptomics-tutorials-with-omicverse：Use this skill to navigate spatial analysis tutorials located under [`T…

spatial-visualization

spatial-visualization。

Statistical Analysis

Statistical Analysis：Statistical analysis是一个systematic process ，用于 testing hypotheses 、 quantifying relationships。 Condu…

statsmodels

statsmodels：Statsmodels is Python's premier 库 ，用于 statistical modeling，providing tools ，用于 estimation，inference，、 diagno…

string-protein-interaction-analysis-with-omicverse

string-protein-interaction-analysis-with-omicverse：Invoke this skill when user has list of genes 、 wants to explore STRI…

SymPy

SymPy是一个Python 库 ，用于 symbolic mathematics that enables exact computation ，使用 mathematical symbols rather than numerical…

time-stepping

time-stepping：Plan 、 control time-step policies ，用于 模拟s。 适合在coupling CFL/physics limits ，支持 adaptive stepping，ramping in…

timesfm-forecasting

timesfm-forecasting：TimesFM (Time Series Foundation Model) is pretrained decoder-only foundation model developed by Goog…

tooluniverse-cancer-variant-interpretation

tooluniverse-cancer-variant-interpretation：提供 comprehensive clinical interpretation of somatic mutations in cancer。 Give…

tooluniverse-clinical-trial-matching

tooluniverse-clinical-trial-matching：AI-driven patient-to-trial matching ，用于 precision medicine 、 oncology。 Given patien…

tooluniverse-epigenomics

tooluniverse-epigenomics：Production-ready genomics 、 epigenomics data processing ，用于 BixBench questions。 Handles methyla…

tooluniverse-gwas-finemapping

tooluniverse-gwas-finemapping：Genome-wide association studies (GWAS) identify genomic regions associated ，支持 traits，but…

tooluniverse-gwas-study-explorer

tooluniverse-gwas-study-explorer：GWAS Study Deep Dive & Meta-Analysis skill enables comprehensive comparison of genome-w…

tooluniverse-image-analysis

tooluniverse-image-analysis：Production-ready microscopy image analysis 、 quantitative imaging data skill ，用于 colony morp…

tooluniverse-immunotherapy-response-prediction

tooluniverse-immunotherapy-response-prediction：预测 patient response to immune checkpoint inhibitors (ICIs) ，使用 multi-biom…

tooluniverse-metabolomics-analysis

tooluniverse-metabolomics-analysis：分析 metabolomics data ，涵盖 metabolite identification，quantification，pathway analysis，、…

tooluniverse-phylogenetics

tooluniverse-phylogenetics：Production-ready phylogenetics 、 sequence analysis skill ，用于 alignment processing，tree analys…

tooluniverse-polygenic-risk-score

tooluniverse-polygenic-risk-score：**Use Cases：** - "Calculate my genetic risk ，用于 type 2 diabetes" - "Build polygenic ri…

tooluniverse-precision-oncology

tooluniverse-precision-oncology：提供 actionable treatment recommendations ，用于 cancer patients based on molecular profile。…

tooluniverse-proteomics-analysis

tooluniverse-proteomics-analysis：分析 mass spectrometry proteomics data ，涵盖 protein quantification，differential expression…

tooluniverse-rnaseq-deseq2

tooluniverse-rnaseq-deseq2：Production-ready RNA-seq differential expression analysis ，使用 PyDESeq2。 执行 DESeq2 normalizati…

tooluniverse-single-cell

tooluniverse-single-cell：Production-ready single-cell 、 expression matrix analysis ，使用 scanpy，anndata，、 scipy。 执行 scRNA-…

tooluniverse-spatial-omics-analysis

tooluniverse-spatial-omics-analysis：Computational analysis 框架 ，用于 spatial multi-omics data integration。 Given spatially…

tooluniverse-statistical-modeling

tooluniverse-statistical-modeling：执行 statistical modeling 、 回归 analysis on biomedical 数据集s。 支持 linear 回归，logistic 回归 (bi…

tooluniverse-variant-analysis

tooluniverse-variant-analysis：Production-ready VCF processing，variant annotation，mutation analysis，、 structural variant…

ukb-navigator

ukb-navigator：Semantic search across UK Biobank's 12，000+ data fields 、 publications — find right variables ，用于 your res…

UMAP-learn

UMAP-learn：UMAP (Uniform Manifold Approximation 、 Projection) is dimensionality reduction technique ，用于 visuali。

usfiscaldata

usfiscaldata：Free，open REST API ，面向 U.S。 Department of Treasury ，用于 federal 金融数据。

Vaex

Vaex是一个high-performance Python 库 designed ，用于 la。

vcf-annotator

vcf-annotator：Annotate VCF variants ，支持 VEP，ClinVar，gnomAD frequencies，、 ancestry-aware context。 生成 prioritised variant…

vcf-statistics

vcf-statistics。

Venue Templates

Venue Templates：访问 comprehensive LaTeX templates，formatting requirements，、 submission guidelines ，用于 major scientific pu…

virtual-lab-agent

virtual-lab-agent：Virtual lab agent ，用于 in silico experiment 模拟 、 protocol optimization。

wikipedia-search

wikipedia-search：检索 、 fetch structured content ，面向 Wikipedia ，使用 MediaWiki API ，用于 reliable，encyclopedic information。

writing

writing：You are **deep research 、 科研写作 assistant** that combines AI-driven research ，支持 well-formatted written outputs。…

xlsx

xlsx：user may ask you to create，edit，或 analy。

XLSX

XLSX：user may ask you to create，edit，或 analy。