数据与复现

aav-vector-design-agent

AAV vector design: capsid selection, promoter optimization, payload capacity.

Adaptyv

Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein s…

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

Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extr…

agentd-drug-discovery

AgentD autonomous drug discovery: target identification, hit finding, ADMET optimization.

alpha-vantage

Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ t…

alphafold

Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences f…

AlphaFold DB

AlphaFold DB is a public repository of AI-predicted 3D protein structures for over 200 million proteins, maintained by D…

AnnData

AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observ…

antibody-design-agent

Antibody design: epitope mapping, CDR engineering, bispecific construction.

Arboreto

Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using parall…

armored-cart-design-agent

Design armored CAR-T cells with cytokine payloads and resistance mechanisms.

arxiv-database

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

arxiv-search

Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic sea…

Astropy

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

autonomous-oncology-agent

Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis gene…

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…

bindcraft

End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in…

binder-design

Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraf…

binding-characterization

Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2)…

bindingdb-database

BindingDB (https://www.bindingdb.org/) is the primary public database of measured drug-protein binding affinities. It co…

bio-admet-prediction

Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG lia…

bio-alignment-files-bam-statistics

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

bio-alignment-filtering

Filter alignments by flag, quality, region, or paired status.

bio-alignment-indexing

Index BAM/CRAM files with samtools index for random access.

bio-alignment-msa-parsing

Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze g…

bio-alignment-msa-statistics

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

bio-alignment-pairwise

Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding…

bio-alignment-sorting

Sort SAM/BAM files by coordinate or name with samtools sort.

bio-alignment-validation

Validate alignment file integrity and detect truncated/corrupt files.

bio-atac-seq-atac-peak-calling

Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying ope…

bio-atac-seq-atac-qc

Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library comple…

bio-atac-seq-differential-accessibility

Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromat…

bio-atac-seq-footprinting

Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identify…

bio-atac-seq-motif-deviation

Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show v…

bio-atac-seq-nucleosome-positioning

Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing c…

bio-basecalling

Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, G…

bio-batch-downloads

Batch download bioinformatics data from NCBI, EBI, Ensembl.

bio-batch-processing

Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences,…

bio-bedgraph-handling

Process bedGraph coverage files: arithmetic, normalization, conversion.

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-cfdna-preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-…

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-motif-analysis

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor bin…

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-peak-calling

ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone mod…

bio-chipseq-qc

ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), libr…

bio-chipseq-super-enhancers

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity gene…

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-clinvar-lookup

Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local V…

bio-clinical-databases-dbsnp-queries

Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsI…

bio-clinical-databases-gnomad-frequencies

Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequ…

bio-clinical-databases-hla-typing

Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining…

bio-clinical-databases-myvariant-queries

Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc…

bio-clinical-databases-pharmacogenomics

Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predict…

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-clinical-databases-somatic-signatures

Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize…

bio-clinical-databases-tumor-mutational-burden

Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when ass…

bio-clinical-databases-variant-prioritization

Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis.…

bio-clip-seq-binding-site-annotation

Annotate CLIP-seq peaks with genomic features and RNA regions.

bio-clip-seq-clip-alignment

Align CLIP-seq reads with STAR; handle unique mappers.

bio-clip-seq-clip-motif-analysis

Discover RBP binding motifs from CLIP-seq peak sequences.

bio-clip-seq-clip-peak-calling

Call RBP binding peaks from CLIP-seq with PureCLIP or MACS2.

bio-clip-seq-clip-preprocessing

Preprocess CLIP-seq/eCLIP data: adapter trimming, demultiplexing.

bio-codon-usage

Analyze codon usage bias and optimize sequences for expression.

bio-comparative-genomics-ancestral-reconstruction

Reconstruct ancestral sequences and traits with ASR methods.

bio-comparative-genomics-hgt-detection

Detect horizontal gene transfer events in microbial genomes.

bio-comparative-genomics-ortholog-inference

Infer orthologs and paralogs with OrthoFinder or OMA.

bio-comparative-genomics-positive-selection

Test for positive selection with PAML, HyPhy, or dN/dS ratios.

bio-comparative-genomics-synteny-analysis

Detect syntenic blocks between genomes with MCScan or SyRI.

bio-compressed-files

Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with.gz or.bz2 sequence f…

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-annotation

Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected g…

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-copy-number-cnvkit-analysis

Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and ge…

bio-copy-number-gatk-cnv

Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV dete…

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-ctdna-mutation-detection

Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-bas…

bio-data-visualization-circos-plots

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

bio-data-visualization-color-palettes

Scientific color palettes: colorblind-safe, perceptually uniform, diverging.

bio-data-visualization-genome-browser-tracks

Generate genome browser tracks and IGV sessions from BAM/BigWig.

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-deseq2-basics

Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating…

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-results

Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying signific…

bio-de-visualization

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

bio-differential-expression-batch-correction

Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch vari…

bio-differential-expression-timeseries-de

Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic ex…

bio-differential-splicing

Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-bas…

bio-duplicate-handling

Mark and remove PCR duplicates with Picard or samtools markdup.

bio-entrez-fetch

Fetch records from NCBI Entrez by accession or UID.

bio-entrez-link

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

bio-entrez-search

Search NCBI Entrez databases (PubMed, gene, nucleotide, protein, SRA).

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-m6a-differential

Differential m6A methylation analysis between conditions.

bio-epitranscriptomics-m6a-peak-calling

Call m6A peaks from MeRIP-seq with exomePeak2 or MACS2.

bio-epitranscriptomics-merip-preprocessing

Preprocess MeRIP-seq data for m6A methylation analysis.

bio-epitranscriptomics-modification-visualization

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

bio-experimental-design-batch-design

Optimize sample batching to minimize confounding with ComBat design.

bio-experimental-design-multiple-testing

Multiple testing correction: Bonferroni, BH/FDR, q-values.

bio-experimental-design-power-analysis

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

bio-experimental-design-sample-size

Power analysis and sample size calculation for omics experiments.

bio-expression-matrix-counts-ingest

Load and validate count matrices from multiple quantification tools.

bio-expression-matrix-gene-id-mapping

Map between Ensembl, Entrez, HGNC, and gene symbol identifiers.

bio-expression-matrix-metadata-joins

Join sample metadata to expression matrices for downstream analysis.

bio-expression-matrix-sparse-handling

Handle sparse count matrices efficiently with scipy sparse formats.

bio-fastq-quality

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-qual…

bio-filter-sequences

Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequence…

bio-flow-cytometry-bead-normalization

Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correct…

bio-flow-cytometry-clustering-phenotyping

Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST w…

bio-flow-cytometry-compensation-transformation

Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application,…

bio-flow-cytometry-cytometry-qc

Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events…

bio-flow-cytometry-differential-analysis

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

bio-flow-cytometry-doublet-detection

Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection…

bio-flow-cytometry-fcs-handling

Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data explo…

bio-flow-cytometry-gating-analysis

Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-drive…

bio-format-conversion

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file fo…

bio-fragment-analysis

Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosom…

bio-gatk-variant-calling

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

bio-genome-assembly-assembly-polishing

Polish assemblies with Medaka (ONT) or NextPolish (Illumina).

bio-genome-assembly-assembly-qc

Assess assembly quality with QUAST, BUSCO, and NGA50 metrics.

bio-genome-assembly-contamination-detection

Detect and remove contamination in assembled genomes.

bio-genome-assembly-hifi-assembly

HiFi (CCS) read assembly with Hifiasm for high-accuracy genomes.

bio-genome-assembly-long-read-assembly

De novo assembly from ONT/PacBio long reads with Flye or Canu.

bio-genome-assembly-metagenome-assembly

Metagenome assembly reconstructs genomes from mixed microbial communities. Long reads enable recovery of complete circul…

bio-genome-assembly-scaffolding

Scaffold contigs with Hi-C, optical mapping, or long reads.

bio-genome-assembly-short-read-assembly

Illumina de novo assembly with SPAdes for metagenomes/bacteria/transcriptomes.

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-genome-intervals-bed-file-basics

Read, write, and filter BED files with pybedtools/bedtools.

bio-genome-intervals-bigwig-tracks

Create and query BigWig signal tracks from BAM/bedGraph.

bio-genome-intervals-coverage-analysis

Compute read depth coverage across genomic regions.

bio-genome-intervals-gtf-gff-handling

Parse and manipulate GTF/GFF annotation files.

bio-genome-intervals-interval-arithmetic

Intersect, subtract, merge, and complement genomic intervals.

bio-genome-intervals-proximity-operations

Find nearest features and compute distances between intervals.

bio-geo-data

Download and parse GEO datasets and series matrices.

bio-hi-c-analysis-compartment-analysis

Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (…

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-data-io

Load, convert, and manipulate Hi-C contact matrices using cooler format. Read.cool/.mcool files, convert from.hic format…

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-hi-c-analysis-loop-calling

Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Ide…

bio-hi-c-analysis-matrix-operations

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), co…

bio-hi-c-analysis-tad-detection

Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Ide…

bio-imaging-mass-cytometry-cell-segmentation

Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for n…

bio-imaging-mass-cytometry-data-preprocessing

Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image n…

bio-imaging-mass-cytometry-phenotyping

Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification…

bio-imaging-mass-cytometry-quality-metrics

Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use w…

bio-imaging-mass-cytometry-spatial-analysis

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

bio-immunoinformatics-epitope-prediction

Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody desi…

bio-immunoinformatics-immunogenicity-scoring

Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, proces…

bio-immunoinformatics-mhc-binding-prediction

Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potent…

bio-immunoinformatics-neoantigen-prediction

Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant…

bio-isoform-switching

Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain chang…

bio-liquid-biopsy-pipeline

Liquid biopsy: cfDNA/ctDNA QC → mutation detection → TMB → MRD.

bio-local-blast

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

bio-long-read-sequencing-clair3-variants

Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline va…

bio-long-read-sequencing-isoseq-analysis

Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript div…

bio-long-read-sequencing-nanopore-methylation

Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA mo…

bio-longitudinal-monitoring

Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fra…

bio-longread-medaka

Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific bas…

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-longread-structural-variants

Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, ins…

bio-machine-learning-biomarker-discovery

Identify biomarkers from omics data with LASSO, elastic net, SHAP.

bio-machine-learning-model-validation

Cross-validation, AUC-ROC, calibration, and permutation testing.

bio-machine-learning-omics-classifiers

Train classifiers on omics data: random forest, SVM, XGBoost.

bio-machine-learning-prediction-explanation

Explain omics ML predictions with SHAP and feature importance.

bio-machine-learning-survival-analysis

Survival ML: RSF, DeepSurv, CoxBoost from omics features.

bio-metabolomics-lipidomics

Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipid…

bio-metabolomics-metabolite-annotation

Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence…

bio-metabolomics-msdial-preprocessing

MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and expor…

bio-metabolomics-normalization-qc

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

bio-metabolomics-pathway-mapping

Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology…

bio-metabolomics-statistical-analysis

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

bio-metabolomics-targeted-analysis

Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, an…

bio-metabolomics-xcms-preprocessing

XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence…

bio-metagenomics-abundance

Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to spec…

bio-metagenomics-amr-detection

Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resi…

bio-metagenomics-functional-profiling

Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene…

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-metaphlan

Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade…

bio-metagenomics-strain-tracking

Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor…

bio-metagenomics-visualization

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

bio-methylation-based-detection

Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Id…

bio-methylation-calling

Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for…

bio-methylation-dmr-detection

Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying…

bio-methylation-methylkit

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

bio-microbiome-amplicon-processing

Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering…

bio-microbiome-differential-abundance

Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsL…

bio-microbiome-diversity-analysis

Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample di…

bio-microbiome-functional-prediction

Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundan…

bio-microbiome-qiime2-workflow

QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in prove…

bio-molecular-descriptors

Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski…

bio-molecular-io

Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structur…

bio-motif-search

Search sequences for regulatory motifs using FIMO, MAST, or regex.

bio-multi-omics-data-harmonization

Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature…

bio-multi-omics-mixomics-analysis

Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for…

bio-multi-omics-mofa-integration

Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view…

bio-multi-omics-similarity-network

Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a…

bio-orchestrator

Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning…

bio-paired-end-fastq

Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs,…

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-gsea

Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coord…

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-pathway-wikipathways

WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated…

bio-pdb-geometric-analysis

Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and…

bio-pdb-structure-io

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloadin…

bio-pdb-structure-modification

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding…

bio-pdb-structure-navigation

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, a…

bio-phasing-imputation-genotype-imputation

Impute missing genotypes using Michigan/TOPMed imputation servers.

bio-phasing-imputation-haplotype-phasing

Phase variants with SHAPEIT4 or BEAGLE.

bio-phasing-imputation-imputation-qc

QC imputed data: R² filter, INFO score, allele concordance.

bio-phylo-distance-calculations

Compute pairwise phylogenetic distances and diversity metrics.

bio-phylo-modern-tree-inference

Maximum likelihood tree inference with IQ-TREE 2 or FastTree.

bio-phylo-tree-io

Read/write phylogenetic trees in Newick, Nexus, PhyloXML formats.

bio-phylo-tree-manipulation

Root, prune, reorder, and annotate phylogenetic trees.

bio-phylo-tree-visualization

Visualize trees with iTOL, ETE3, or ggtree.

bio-pileup-generation

Generate base-level pileup from BAM for variant calling and coverage.

bio-population-genetics-association-testing

GWAS association testing with PLINK, BOLT-LMM, or SAIGE.

bio-population-genetics-linkage-disequilibrium

Compute LD metrics (r², D') and LD decay analysis.

bio-population-genetics-plink-basics

PLINK2 for GWAS QC, LD pruning, and basic population genetics.

bio-population-genetics-population-structure

Population stratification with PCA, ADMIXTURE, and STRUCTURE.

bio-population-genetics-scikit-allel-analysis

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

bio-population-genetics-selection-statistics

Detect natural selection signatures: iHS, XP-EHH, Tajima's D.

bio-primer-design-primer-basics

Design PCR primers with Primer3 for standard amplification.

bio-primer-design-primer-validation

Validate primer specificity by BLAST and thermodynamic analysis.

bio-primer-design-qpcr-primers

Design qPCR/RT-PCR primers with efficiency and specificity optimization.

bio-proteomics-data-import

Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant prote…

bio-proteomics-dia-analysis

Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrom…

bio-proteomics-differential-abundance

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

bio-proteomics-peptide-identification

Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spe…

bio-proteomics-protein-inference

Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides.…

bio-proteomics-proteomics-qc

Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analys…

bio-proteomics-ptm-analysis

Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localiz…

bio-proteomics-quantification

Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT,…

bio-proteomics-spectral-libraries

Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DI…

bio-reaction-enumeration

Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries…

bio-read-alignment-bowtie2-alignment

Align short reads with Bowtie2; local and end-to-end modes.

bio-read-alignment-hisat2-alignment

Splice-aware RNA-seq alignment with HISAT2.

bio-read-alignment-star-alignment

High-speed STAR aligner for RNA-seq with junction detection.

bio-read-qc-adapter-trimming

Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Il…

bio-read-qc-fastp-workflow

All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction,…

bio-read-qc-quality-filtering

Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove…

bio-read-qc-quality-reports

Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter conte…

bio-read-qc-umi-processing

Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep…

bio-read-sequences

Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing seque…

bio-reporting-automated-qc-reports

Generate automated MultiQC-style reports for omics pipelines.

bio-reporting-figure-export

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

bio-reporting-jupyter-reports

Create Jupyter notebook reports with reproducible analysis code.

bio-reporting-quarto-reports

Build Quarto multi-format reports (HTML/PDF) from analysis code.

bio-reporting-rmarkdown-reports

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

bio-research-tools-biomarker-signature-studio

Build, validate, and visualize multi-omic biomarker signatures.

bio-restriction-enzyme-selection

Select restriction enzymes for cloning based on cut sites and compatibility.

bio-restriction-fragment-analysis

Analyze restriction fragment patterns for cloning and gel prediction.

bio-restriction-mapping

Create restriction maps and in silico digestion patterns.

bio-restriction-sites

Find restriction enzyme recognition sites in DNA sequences.

bio-reverse-complement

Compute reverse complement and strand-aware sequence operations.

bio-ribo-seq-orf-detection

Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use w…

bio-ribo-seq-riboseq-preprocessing

Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when pre…

bio-ribo-seq-ribosome-periodicity

Validate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing l…

bio-ribo-seq-ribosome-stalling

Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regul…

bio-ribo-seq-translation-efficiency

Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translati…

bio-rna-quantification-alignment-free-quant

Pseudo-alignment quantification with Salmon or Kallisto.

bio-rna-quantification-count-matrix-qc

QC count matrices: library size, zero inflation, gene detection rates.

bio-rna-quantification-featurecounts-counting

Count reads per gene with featureCounts from subread package.

bio-rna-quantification-tximport-workflow

Import Salmon/Kallisto quantification into R/DESeq2 with tximport.

bio-rnaseq-qc

RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage,…

bio-sam-bam-basics

Read, inspect, and manipulate SAM/BAM files with samtools/pysam.

bio-sashimi-plots

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

bio-seq-objects

Work with BioPython sequence objects: SeqRecord, features, annotations.

bio-sequence-properties

Compute sequence properties: MW, pI, hydrophobicity, extinction coefficient.

bio-sequence-similarity

Compute sequence similarity with pairwise alignment and percent identity.

bio-sequence-slicing

Slice, extract, and manipulate subsequences from FASTA/FASTQ.

bio-sequence-statistics

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

bio-similarity-searching

Performs molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar…

bio-single-cell-batch-integration

Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variatio…

bio-single-cell-cell-annotation

Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for cons…

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-clustering

Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PC…

bio-single-cell-data-io

Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data…

bio-single-cell-doublet-detection

Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python…

bio-single-cell-lineage-tracing

Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics…

bio-single-cell-markers-annotation

Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for different…

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-single-cell-multimodal-integration

Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple mo…

bio-single-cell-perturb-seq

Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function thr…

bio-single-cell-preprocessing

Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for calc…

bio-single-cell-scatac-analysis

Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensiona…

bio-single-cell-splicing

Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for…

bio-single-cell-trajectory-inference

Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for…

bio-small-rna-seq-differential-mirna

Differential miRNA expression analysis with DESeq2/edgeR.

bio-small-rna-seq-mirdeep2-analysis

Identify and quantify known/novel miRNAs with miRDeep2.

bio-small-rna-seq-mirge3-analysis

miRNA annotation and quantification with miRge3.0.

bio-small-rna-seq-smrna-preprocessing

Preprocess small RNA-seq: adapter trimming, size selection.

bio-small-rna-seq-target-prediction

Predict miRNA target genes with TargetScan or miRDB.

bio-spatial-transcriptomics-image-analysis

Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells…

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-data-io

Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and Spatial…

bio-spatial-transcriptomics-spatial-deconvolution

Deconvolution estimates cell type proportions in each spatial spot using a reference single-cell dataset. Essential for…

bio-spatial-transcriptomics-spatial-domains

Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots cons…

bio-spatial-transcriptomics-spatial-multiomics

Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular r…

bio-spatial-transcriptomics-spatial-neighbors

Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay tria…

bio-spatial-transcriptomics-spatial-preprocessing

Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics,…

bio-spatial-transcriptomics-spatial-proteomics

Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalizat…

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-splicing-pipeline

Alternative splicing analysis: rMATS → PSI → differential → sashimi.

bio-splicing-qc

Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring,…

bio-splicing-quantification

Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-t…

bio-sra-data

Download raw sequencing data from NCBI SRA with fasterq-dump.

bio-structural-biology-alphafold-predictions

Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins withou…

bio-structural-biology-modern-structure-prediction

Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predictin…

bio-substructure-search

Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacopho…

bio-systems-biology-context-specific-models

Build context-specific metabolic models from expression data (GIMME, iMAT).

bio-systems-biology-flux-balance-analysis

Flux balance analysis (FBA) with COBRApy for metabolic network modeling.

bio-systems-biology-gene-essentiality

Predict essential genes by single gene knockouts in metabolic models.

bio-systems-biology-metabolic-reconstruction

Reconstruct genome-scale metabolic models from genome annotations.

bio-systems-biology-model-curation

Curate SBML metabolic models: mass/charge balance, gap filling.

bio-tcr-bcr-analysis-immcantation-analysis

Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation fram…

bio-tcr-bcr-analysis-mixcr-analysis

Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune…

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-tcr-bcr-analysis-scirpy-analysis

Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VD…

bio-tcr-bcr-analysis-vdjtools-analysis

Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analy…

bio-transcription-translation

Transcribe and translate DNA sequences; handle genetic code variations.

bio-tumor-fraction-estimation

Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number altera…

bio-uniprot-access

Query UniProt for protein sequences, annotations, and cross-references.

bio-variant-annotation

Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predic…

bio-variant-calling

Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or g…

bio-variant-calling-clinical-interpretation

Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for di…

bio-variant-calling-deepvariant

Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Il…

bio-variant-calling-filtering-best-practices

Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretati…

bio-variant-calling-joint-calling

Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies,…

bio-variant-calling-structural-variant-calling

Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions,…

bio-variant-normalization

Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from dif…

bio-vcf-basics

View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting sp…

bio-vcf-manipulation

Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing ca…

bio-vcf-statistics

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

bio-virtual-screening

Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files,…

bio-workflow-management-cwl-workflows

Write Common Workflow Language (CWL) portable workflow definitions.

bio-workflow-management-nextflow-pipelines

Build and run Nextflow (DSL2) bioinformatics pipelines.

bio-workflow-management-snakemake-workflows

Create and manage Snakemake reproducible bioinformatics workflows.

bio-workflow-management-wdl-workflows

Create WDL workflows for Terra/Cromwell bioinformatics execution.

bio-workflows-atacseq-pipeline

ATAC-seq: trimming → alignment → peak calling → differential.

bio-workflows-biomarker-pipeline

Biomarker discovery: omics → feature selection → validation → report.

bio-workflows-chipseq-pipeline

ChIP-seq: alignment → peak calling → motif analysis → annotation.

bio-workflows-clip-pipeline

CLIP-seq: peak calling → binding site annotation → motif discovery.

bio-workflows-cnv-pipeline

Copy number variant detection: WGS/WES CNV calling and annotation.

bio-workflows-crispr-editing-pipeline

CRISPR editing: amplicon sequencing → CRISPResso2 → outcome analysis.

bio-workflows-crispr-screen-pipeline

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

bio-workflows-cytometry-pipeline

Flow/mass cytometry: QC → gating → clustering → differential.

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-fastq-to-variants

Complete FASTQ → alignment → variant calling pipeline.

bio-workflows-genome-assembly-pipeline

De novo genome assembly: raw reads → assembly → QC → annotation.

bio-workflows-gwas-pipeline

GWAS: QC → imputation → association → fine-mapping → annotation.

bio-workflows-hic-pipeline

Hi-C contact map generation, normalization, TAD/loop calling.

bio-workflows-imc-pipeline

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

bio-workflows-longread-sv-pipeline

Long-read structural variant calling and annotation pipeline.

bio-workflows-merip-pipeline

MeRIP-seq: m6A peak calling → differential → motif 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。

bio-workflows-metagenomics-pipeline

Metagenomics: QC → classification → functional profiling → AMR.

bio-workflows-methylation-pipeline

WGBS/RRBS: bismark alignment → methylation calling → DMR detection.

bio-workflows-microbiome-pipeline

Microbiome: 16S/ITS amplicon or shotgun → diversity → differential.

bio-workflows-multi-omics-pipeline

Multi-omics integration pipeline: MOFA, SNF, similarity network fusion.

bio-workflows-multiome-pipeline

10x Multiome: joint scRNA-seq + scATAC-seq processing and integration.

bio-workflows-neoantigen-pipeline

Neoantigen prediction: somatic variants → MHC binding → immunogenicity.

bio-workflows-outbreak-pipeline

Pathogen genomics: assembly → typing → phylodynamics → transmission.

bio-workflows-proteomics-pipeline

DDA/DIA proteomics: search → quantification → differential abundance.

bio-workflows-riboseq-pipeline

Ribo-seq: footprint alignment → periodicity → ORF detection.

bio-workflows-rnaseq-to-de

RNA-seq → alignment → counts → DESeq2 differential expression.

bio-workflows-scrnaseq-pipeline

Single-cell RNA-seq end-to-end: Cell Ranger → Scanpy → clustering.

bio-workflows-smrna-pipeline

Small RNA-seq: miRNA identification → quantification → DE analysis.

bio-workflows-somatic-variant-pipeline

Tumor-normal somatic variant calling with GATK Mutect2/Strelka2.

bio-workflows-spatial-pipeline

Spatial transcriptomics: alignment → deconvolution → domain detection.

bio-workflows-tcr-pipeline

TCR/BCR: V(D)J alignment → clonotype → repertoire analysis.

bio-write-sequences

Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences,…

bioinformatics-singlecell

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

biokernel

BioKernel: unified computational kernel for bioinformatics tool orchestration.

biomaster-workflows

BioMaster workflow orchestration for end-to-end bioinformatics analyses.

biomcp-server

BioMCP: Model Context Protocol server for bioinformatics tool access.

biomedical-data-analysis

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

biomedical-search

Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Val…

biomni

Biomni is an open-source biomedical AI agent framework from Stanford's SNAP lab that autonomously executes complex resea…

biomni-general-agent

BioMni general biomedical agent for flexible multi-step research tasks.

BioServices

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

boltz

Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predictin…

boltzgen

All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the s…

bone-marrow-ai-agent

Bone marrow analysis: blast counting, immunophenotyping, disease classification.

BRENDA

BRENDA (BRaunschweig ENzyme DAtabase) is the world's most comprehensive enzyme information system, containing detailed e…

bulk-rna-seq-batch-correction-with-combat

Apply this skill when a user has multiple bulk expression matrices measured across different batches and needs to harmon…

bulk-rna-seq-deconvolution-with-bulk2single

Use this skill when a user wants to reconstruct single-cell profiles from bulk RNA-seq together with a matched reference…

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…

bulk-wgcna-analysis-with-omicverse

Activate this skill for users who want to reproduce the WGCNA workflow from [`t_wgcna.ipynb`](../../omicverse_guide/docs…

bulktrajblend-trajectory-interpolation

Invoke this skill when users need to bridge gaps in single-cell developmental trajectories using matched bulk RNA-seq. I…

cancer-metabolism-agent

Analyze tumor metabolic reprogramming from transcriptomic and metabolomic data.

care-coordination

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

cart-design-optimizer-agent

Optimize CAR-T cell construct design: scFv selection, linker, co-stimulatory domain.

cbioportal-database

cBioPortal for Cancer Genomics (https://www.cbioportal.org/) is an open-access resource for exploring, visualizing, and…

cell-free-expression

Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooti…

cellagent-annotation

AI-driven single-cell cluster annotation using marker gene databases.

cellfree-rna-agent

Cell-free RNA analysis: plasma cfRNA profiling for liquid biopsy diagnostics.

cellular-senescence-agent

cellular-senescence-agent：Cellular senescence analysis：marker scoring，SASP profiling，tissue aging assessment。

Cellxgene Census

The C.

chai

Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting prote…

chatehr-clinician-assistant

EHR clinical assistant: note summarization, structured data extraction, clinical decision support.

chematagent-drug-discovery

CheMatAgent: chemistry-aware drug design with retrosynthesis and property optimization.

ChEMBL

ChEMBL is a manually curated database of bioactive molecules maintained by the European Bioinformatics Institute (EBI),…

chembl-search

Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu seman…

chemcrow-drug-discovery

ChemCrow drug discovery toolkit: web search, Python, chemical tools integration.

chemical-property-lookup

Look up chemical properties from PubChem, ChEMBL, DrugBank by name/SMILES.

chemistry-agent

General chemistry agent for synthesis planning, reaction prediction, and property calculation.

chip-clonal-hematopoiesis-agent

Clonal hematopoiesis of indeterminate potential (CHIP) variant detection and risk assessment.

chromosomal-instability-agent

Quantify chromosomal instability (CIN) from copy number and SV data.

Citation Management

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

claims-appeals

Insurance claims appeals: documentation preparation and denial reasoning analysis.

claw-ancestry-pca

Ancestry decomposition PCA against the Simons Genome Diversity Project.

claw-metagenomics

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways.

claw-semantic-sim

Semantic Similarity Index for disease research literature using PubMedBERT embeddings.

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…

clinical-interpretation

clinical-interpretation.

clinical-nlp-extractor

Extract clinical entities (diagnoses, medications, procedures) from unstructured text.

clinical-note-summarization

Summarize clinical notes into structured SOAP format with key findings.

clinical-trial-protocol-skill

This skill generates clinical trial protocols for **medical devices or drugs** using a **modular, waypoint-based archite…

clinical-trials-search

Search ClinicalTrials.gov with natural language queries. Find clinical trials, enrollment, and outcomes using Valyu sema…

clinicaltrials-database

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

clinpgx

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels.

ClinPGx

ClinPGx (Clinical Pharmacogenomics Database) is a comprehensive resource for clinical pharmacogenomics information, succ…

ClinVar

ClinVar is NCBI's freely accessible archive of reports on relationships between human genetic variants and phenotypes, w…

cnv-caller-agent

Specialized CNV detection agent integrating multiple callers with ensemble scoring.

coagulation-thrombosis-agent

Coagulation pathway analysis, thrombophilia assessment, anticoagulation guidance.

COBRApy

COBRApy is a Python library for constraint-based reconstruction and analysis (COBRA) of metabolic models, essential for…

compbioagent-explorer

Computational biology exploration agent for multi-omics dataset analysis.

computational-pathology-agent

This agent speciali.

consciousness-council

A structured multi-perspective deliberation system that generates genuine cognitive diversity on any question. Instead o…

consensus-sequences

consensus-sequences。

convergence-study

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

COSMIC

COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring s…

crispr-guide-design

CRISPR guide RNA design with on-target scoring and off-target minimization.

crispr-offtarget-predictor

Predict CRISPR Cas9/Cas12 off-target sites genome-wide with CRISPOR/Cas-OFFinder.

cryoem-ai-drug-design-agent

AI-guided drug design from cryo-EM structures: binding site analysis and docking.

ctdna-dynamics-mrd-agent

Track ctDNA dynamics for minimal residual disease detection and treatment monitoring.

cytokine-storm-analysis-agent

Cytokine storm detection, severity scoring, and intervention modeling.

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…

Datamol

Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminforma…

deep-visual-proteomics-agent

Deep visual proteomics: spatial proteomic analysis from laser-capture microdissection MS data.

DeepChem

DeepChem is a comprehensive Python library for applying machine learning to chemistry, materials science, and biology. E…

deepTools

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

deepvariant

deepvariant.

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…

depmap

The Cancer Dependency Map (DepMap) project, run by the Broad Institute, systematically characteri.

dhdna-profiler

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

DiffDock

DiffDock is a diffusion-based deep learning tool for molecular docking that predicts 3D binding poses of small molecule…

differentiation-schemes

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

digital-twin-clinical-agent

Create patient digital twins for treatment simulation and outcome prediction.

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

A.docx file is a.

docx

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

drug-discovery-search

End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language power…

drug-interaction-checker

Check drug-drug interactions from patient medication lists with severity scoring.

drug-labels-search

Search FDA drug labels with natural language queries. Official drug information, indications, and safety data via Valyu.

drug-photo

Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance.

DrugBank

DrugBank is a comprehensive bioinformatics and cheminformatics database containing detailed information on drugs and dru…

drugbank-search

Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety dat…

edgartools

Python library for accessing all SEC filings since 1994 with structured data extraction.

ehr-fhir-integration

EHR-FHIR integration: HL7 FHIR resource creation, querying, and workflow automation.

ena-database

The European Nucleotide Archive (ENA) is a comprehensive public repository for nucleotide sequence data and associated m…

Ensembl

Access and query the Ensembl genome database, a comprehensive resource for vertebrate genomic data maintained by EMBL-EB…

epigenomics-methylgpt-agent

Epigenomics and DNA methylation analysis with MethylGPT-inspired approaches.

equity-scorer

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

esm

ESM provides state-of-the-art protein language models for understanding, generating, and designing proteins. This skill…

etetoolkit

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

exosome-ev-analysis-agent

Extracellular vesicle and exosome analysis: cargo profiling and biomarker discovery.

Exploratory Data Analysis

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

fastq-analysis-pipeline

OmicVerse provides a complete FASTQ-to-count-matrix pipeline via the `ov.alignment` module. This skill covers: - **SRA d…

fda-database

Access comprehensive FDA regulatory data through openFDA, the FDA's initiative to provide open APIs for public datasets.…

fhir-developer-skill

FHIR API development guide for building healthcare endpoints. Use when: (1) Creating FHIR REST endpoints (Patient, Obser…

fhir-development

FHIR API development: build SMART on FHIR apps and FHIR resource endpoints.

filtering-best-practices

filtering-best-practices。

find-skills

Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is th…

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…

foldseek

Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2…

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…

galaxy-bridge

Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with m…

gatk-variant-calling

gatk-variant-calling.

gene-panel-design-agent

Design targeted gene panels for clinical or research sequencing applications.

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…

geniml

Geniml is a Python package for building machine learning models on genomic interval data from BED files. It provides uns…

genome-compare

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture.

geo-database

The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomic…

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 ，…

gget

gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and anal…

Ginkgo Cloud Lab

Ginkgo Cloud Lab (https://cloud.ginkgo.bio) provides remote access to Ginkgo Bioworks' autonomous lab infrastructure. Pr…