Data & Reproduction

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 sequences via API or…

aeon

Aeon is a scikit-learn compatible Python toolkit for time series machine learning. It provides state-of-the-art algorithms for classificatio…

agent-browser

Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…

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+ technical indicators.

alphafold

Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) P…

AlphaFold DB

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

AnnData

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

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 paralleli.

armored-cart-design-agent

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

arxiv-database

This skill provides Python tools for searching and retrieving preprints from arXiv.org via its public Atom API. It supports keyword search,…

arxiv-search

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

Astropy

Astropy is the core Python package for astronomy, providing essential functionality for astronomical research and data analysis. Use astropy…

autonomous-oncology-agent

Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis generation.

bayesian-optimizer

Bayesian optimization for experimental design and hyperparameter tuning in biomedical research.

Benchling Integration

Benchling is a cloud platform for life sciences R&D. Access registry entities (DNA, proteins), inventory, electronic lab notebooks, and work…

bgpt-paper-search

BGPT is a remote MCP server that searches a curated database of scientific papers built from raw experimental data extracted from full-text…

bindcraft

End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2)…

binder-design

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

binding-characterization

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

bindingdb-database

BindingDB (https://www.bindingdb.org/) is the primary public database of measured drug-protein binding affinities. It contains over 3 millio…

bio-admet-prediction

Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxi…

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 gaps, work with annot…

bio-alignment-msa-statistics

Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when com…

bio-alignment-pairwise

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

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 open chromatin regions…

bio-atac-seq-atac-qc

Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when asses…

bio-atac-seq-differential-accessibility

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

bio-atac-seq-footprinting

Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy pat…

bio-atac-seq-motif-deviation

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

bio-atac-seq-nucleosome-positioning

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

bio-basecalling

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

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, or automating file…

bio-bedgraph-handling

Process bedGraph coverage files: arithmetic, normalization, conversion.

bio-blast-searches

Run BLAST searches against local or remote databases for sequence homology.

bio-causal-genomics-colocalization-analysis

Colocali.

bio-causal-genomics-fine-mapping

Fine-mapping narrows GWAS association signals to identify likely causal variants. Key outputs: - **PIP** (Posterior Inclusion Probability) -…

bio-causal-genomics-mediation-analysis

Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expre…

bio-causal-genomics-mendelian-randomization

Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR…

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-aware duplicate remo…

bio-chipseq-differential-binding

Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples.…

bio-chipseq-motif-analysis

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

bio-chipseq-peak-annotation

Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. F…

bio-chipseq-peak-calling

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

bio-chipseq-qc

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

bio-chipseq-super-enhancers

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

bio-chipseq-visualization

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal a…

bio-clinical-databases-clinvar-lookup

Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determi…

bio-clinical-databases-dbsnp-queries

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

bio-clinical-databases-gnomad-frequencies

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

bio-clinical-databases-hla-typing

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

bio-clinical-databases-myvariant-queries

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

bio-clinical-databases-pharmacogenomics

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

bio-clinical-databases-polygenic-risk

Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genom…

bio-clinical-databases-somatic-signatures

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

bio-clinical-databases-tumor-mutational-burden

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

bio-clinical-databases-variant-prioritization

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

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 files. Use BGZF for i…

bio-consensus-sequences

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific refer…

bio-copy-number-cnv-annotation

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

bio-copy-number-cnv-visualization

Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or oth…

bio-copy-number-cnvkit-analysis

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

bio-copy-number-gatk-cnv

Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WE…

bio-crispr-screens-base-editing-analysis

Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies. Use when quantifying…

bio-crispr-screens-batch-correction

Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use…

bio-crispr-screens-crispresso-editing

CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports. Use…

bio-crispr-screens-hit-calling

Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and re…

bio-crispr-screens-jacks-analysis

JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR…

bio-crispr-screens-library-design

CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designi…

bio-crispr-screens-mageck-analysis

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene rankin…

bio-crispr-screens-screen-qc

Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recov…

bio-ctdna-mutation-detection

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

bio-data-visualization-circos-plots

Circular genome visualization with Circos or 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

Multi-panel genome track plots with pyGenomeTracks.

bio-data-visualization-ggplot2-fundamentals

R ggplot2 for publication-quality genomics and omics figures.

bio-data-visualization-heatmaps-clustering

Hierarchical clustering heatmaps with ComplexHeatmap or seaborn.

bio-data-visualization-interactive-visualization

Interactive omics visualizations with Plotly, Bokeh, or shiny.

bio-data-visualization-multipanel-figures

Compose multipanel publication figures with cowplot or patchwork.

bio-data-visualization-specialized-omics-plots

Specialized plots: lollipop (mutations), circomap, oncoprint.

bio-data-visualization-upset-plots

UpSet plots for multi-set intersection visualization.

bio-data-visualization-volcano-customization

Customized volcano plots with ggplot2 or matplotlib for DE results.

bio-de-deseq2-basics

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

bio-de-edger-basics

Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-tes…

bio-de-results

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

bio-de-visualization

Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample di…

bio-differential-expression-batch-correction

Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when corr…

bio-differential-expression-timeseries-de

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

bio-differential-splicing

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

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

Retrieve linked records across NCBI Entrez databases.

bio-entrez-search

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

bio-epidemiological-genomics-amr-surveillance

Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends an…

bio-epidemiological-genomics-pathogen-typing

Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst…

bio-epidemiological-genomics-phylodynamics

Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times…

bio-epidemiological-genomics-transmission-inference

Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimat…

bio-epidemiological-genomics-variant-surveillance

Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify eme…

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

Visualize RNA modification profiles and 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

Statistical power analysis for 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-quality bases, or genera…

bio-filter-sequences

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

bio-flow-cytometry-bead-normalization

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

bio-flow-cytometry-clustering-phenotyping

Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when d…

bio-flow-cytometry-compensation-transformation

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

bio-flow-cytometry-cytometry-qc

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

bio-flow-cytometry-differential-analysis

Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use whe…

bio-flow-cytometry-doublet-detection

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

bio-flow-cytometry-fcs-handling

Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loa…

bio-flow-cytometry-gating-analysis

Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when id…

bio-format-conversion

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

bio-fragment-analysis

Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patter…

bio-gatk-variant-calling

Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint geno…

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 circular genomes and resol…

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

Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positio…

bio-genome-engineering-grna-design

Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity usin…

bio-genome-engineering-hdr-template-design

Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimi…

bio-genome-engineering-off-target-prediction

Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and…

bio-genome-engineering-prime-editing-design

Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modificat…

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 (B) chromatin compart…

bio-hi-c-analysis-contact-pairs

Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequ…

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, access matrix data…

bio-hi-c-analysis-hic-differential

Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical sig…

bio-hi-c-analysis-hic-visualization

Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virt…

bio-hi-c-analysis-loop-calling

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

bio-hi-c-analysis-matrix-operations

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

bio-hi-c-analysis-tad-detection

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

bio-imaging-mass-cytometry-cell-segmentation

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

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 normalization. Use wh…

bio-imaging-mass-cytometry-phenotyping

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

bio-imaging-mass-cytometry-quality-metrics

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

bio-imaging-mass-cytometry-spatial-analysis

Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Us…

bio-immunoinformatics-epitope-prediction

Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunog…

bio-immunoinformatics-immunogenicity-scoring

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

bio-immunoinformatics-mhc-binding-prediction

Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes…

bio-immunoinformatics-neoantigen-prediction

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

bio-isoform-switching

Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity,…

bio-liquid-biopsy-pipeline

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

bio-local-blast

Set up and run BLAST+ locally with 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 variants from ONT or P…

bio-long-read-sequencing-isoseq-analysis

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

bio-long-read-sequencing-nanopore-methylation

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

bio-longitudinal-monitoring

Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutati…

bio-longread-medaka

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

bio-longread-qc

Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality…

bio-longread-structural-variants

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

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 lipidomics with LipidSear…

bio-metabolomics-metabolite-annotation

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

bio-metabolomics-msdial-preprocessing

MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream ana…

bio-metabolomics-normalization-qc

Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods.…

bio-metabolomics-pathway-mapping

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

bio-metabolomics-statistical-analysis

Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when…

bio-metabolomics-targeted-analysis

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

bio-metabolomics-xcms-preprocessing

XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap…

bio-metagenomics-abundance

Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurat…

bio-metagenomics-amr-detection

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

bio-metagenomics-functional-profiling

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

bio-metagenomics-kraken

Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing in…

bio-metagenomics-metaphlan

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

bio-metagenomics-strain-tracking

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

bio-metagenomics-visualization

Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plot…

bio-methylation-based-detection

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

bio-methylation-calling

Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH c…

bio-methylation-dmr-detection

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

bio-methylation-methylkit

DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical…

bio-microbiome-amplicon-processing

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

bio-microbiome-differential-abundance

Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identi…

bio-microbiome-diversity-analysis

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

bio-microbiome-functional-prediction

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

bio-microbiome-qiime2-workflow

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

bio-molecular-descriptors

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

bio-molecular-io

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

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 alignment, and missi…

bio-multi-omics-mixomics-analysis

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

bio-multi-omics-mofa-integration

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

bio-multi-omics-similarity-network

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

bio-orchestrator

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

bio-paired-end-fastq

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

bio-pathway-enrichment-visualization

Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results.…

bio-pathway-go-enrichment

Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list…

bio-pathway-gsea

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

bio-pathway-kegg-pathways

KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling p…

bio-pathway-reactome

Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway databas…

bio-pathway-wikipathways

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

bio-pdb-geometric-analysis

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

bio-pdb-structure-io

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RC…

bio-pdb-structure-modification

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

bio-pdb-structure-navigation

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

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

Population genetics analysis with 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 proteinGroups.txt. Use wh…

bio-proteomics-dia-analysis

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

bio-proteomics-differential-abundance

Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correc…

bio-proteomics-peptide-identification

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

bio-proteomics-protein-inference

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

bio-proteomics-proteomics-qc

Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analysis. Covers sample me…

bio-proteomics-ptm-analysis

Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysi…

bio-proteomics-quantification

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

bio-proteomics-spectral-libraries

Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers D…

bio-reaction-enumeration

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

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, Illumina TruSeq, Nexte…

bio-read-qc-fastp-workflow

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

bio-read-qc-quality-filtering

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

bio-read-qc-quality-reports

Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplica…

bio-read-qc-umi-processing

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

bio-read-sequences

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

bio-reporting-automated-qc-reports

Generate automated MultiQC-style reports for omics pipelines.

bio-reporting-figure-export

Export publication-quality figures 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

Render Rmarkdown reports with integrated plots and 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 when identifying tran…

bio-ribo-seq-riboseq-preprocessing

Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq read…

bio-ribo-seq-ribosome-periodicity

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

bio-ribo-seq-ribosome-stalling

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

bio-ribo-seq-translation-efficiency

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

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, and transcript integ…

bio-sam-bam-basics

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

bio-sashimi-plots

Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot. Visualizes differential…

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

Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets,…

bio-similarity-searching

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

bio-single-cell-batch-integration

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

bio-single-cell-cell-annotation

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

bio-single-cell-cell-communication

Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use…

bio-single-cell-clustering

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

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, importing/exportin…

bio-single-cell-doublet-detection

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

bio-single-cell-lineage-tracing

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

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 differential expression betwe…

bio-single-cell-metabolite-communication

Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types. Predict metabolite…

bio-single-cell-multimodal-integration

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

bio-single-cell-perturb-seq

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

bio-single-cell-preprocessing

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

bio-single-cell-scatac-analysis

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

bio-single-cell-splicing

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

bio-single-cell-trajectory-inference

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

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/nuclei, and compute…

bio-spatial-transcriptomics-spatial-communication

Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling,…

bio-spatial-transcriptomics-spatial-data-io

Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ran…

bio-spatial-transcriptomics-spatial-deconvolution

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

bio-spatial-transcriptomics-spatial-domains

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

bio-spatial-transcriptomics-spatial-multiomics

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

bio-spatial-transcriptomics-spatial-neighbors

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

bio-spatial-transcriptomics-spatial-preprocessing

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

bio-spatial-transcriptomics-spatial-proteomics

Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when workin…

bio-spatial-transcriptomics-spatial-statistics

Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occur…

bio-spatial-transcriptomics-spatial-visualization

Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlai…

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, and junction coverag…

bio-splicing-quantification

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

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 without experimental struc…

bio-structural-biology-modern-structure-prediction

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

bio-substructure-search

Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functio…

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 framework. Use when stud…

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 repertoire sequencin…

bio-tcr-bcr-analysis-repertoire-visualization

Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network gra…

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 VDJ data alongside scR…

bio-tcr-bcr-analysis-vdjtools-analysis

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

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 alterations via HMM segmen…

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, predict functional consequ…

bio-variant-calling

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

bio-variant-calling-clinical-interpretation

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

bio-variant-calling-deepvariant

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

bio-variant-calling-filtering-best-practices

Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and inde…

bio-variant-calling-joint-calling

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

bio-variant-calling-structural-variant-calling

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

bio-variant-normalization

Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or pr…

bio-vcf-basics

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

bio-vcf-manipulation

Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restruct…

bio-vcf-statistics

Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality,…

bio-virtual-screening

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

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

CRISPR screen: guide counting → MAGeCK → hit calling → visualization.

bio-workflows-cytometry-pipeline

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

bio-workflows-expression-to-pathways

End-to-end workflow from differential expression to GO/KEGG/Reactome enrichment and pathway visualization.

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

Imaging mass cytometry: segmentation → 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

Metabolic model reconstruction → FBA → simulation → visualization.

bio-workflows-metabolomics-pipeline

LC-MS/GC-MS: preprocessing → annotation → statistical analysis.

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, creating new sequenc…

bioinformatics-singlecell

General single-cell bioinformatics: clustering, 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

Comprehensive biomedical data analysis: statistics, visualization, and interpretation.

biomedical-search

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

biomni

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

biomni-general-agent

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

BioServices

BioServices is a Python package providing programmatic access to approximately 40 bioinformatics web services and databases. Retrieve biolog…

boltz

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

boltzgen

All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing…

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 enzyme data from scie…

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 harmonise them before down…

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 scRNA-seq atlas. It…

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

Use this skill when a user wants to reproduce the DESeq2 workflow showcased in [`t_deseq2.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/…

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

Follow this skill to run the end-to-end differential expression (DEG) workflow showcased in [`t_deg.ipynb`](../../omicverse_guide/docs/Tutor…

bulk-wgcna-analysis-with-omicverse

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

bulktrajblend-trajectory-interpolation

Invoke this skill when users need to bridge gaps in single-cell developmental trajectories using matched bulk RNA-seq. It follows [`t_bulktr…

cancer-metabolism-agent

Analyze tumor metabolic reprogramming from transcriptomic and metabolomic data.

care-coordination

Care coordination agent: multi-disciplinary team communication and 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 analyzing multidimen…

cell-free-expression

Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggr…

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 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 protein-protein complex s…

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), containing over 2 mi…

chembl-search

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

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

Manage citations systematically throughout the research and writing process. This skill provides tools and strategies for searching academic…

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

Generate professional clinical decision support (CDS) documents for pharmaceutical companies, clinical researchers, and medical decision-mak…

Clinical Reports

Clinical report writing is the process of documenting medical information with precision, accuracy, and compliance with regulatory standards…

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 architecture**.

clinical-trials-search

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

clinicaltrials-database

ClinicalTrials.gov is a comprehensive registry of clinical studies conducted worldwide, maintained by the U.S. National Library of Medicine.…

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, successor to PharmGKB. I…

ClinVar

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

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 systems biology rese…

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 of one voice giving o…

consensus-sequences

consensus-sequences.

convergence-study

Spatial and temporal convergence analysis with Richardson extrapolation and Grid Convergence Index (GCI) for solution verification.

COSMIC

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

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 is a Python library for parallel and distributed computing that enables three critical capabilities: - **Larger-than-memory execution**…

Data Commons

Use the `idc-index` Python package to query and download public cancer imaging data from the National Cancer Institute Imaging Data Commons…

data-stats-analysis

This skill enables you to perform rigorous statistical analyses including t-tests, ANOVA, correlation analysis, hypothesis testing, and mult…

data-transform

This skill enables you to perform comprehensive data transformations including cleaning, normali.

data-visualization-biomedical

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

data-visualization-expert

Expert data visualization for complex scientific and clinical datasets.

data-viz-plots

This skill enables you to create professional scientific visuali.

datacommons-client

Provides comprehensive access to the Data Commons Python API v2 for querying statistical observations, exploring the knowledge graph, and re…

Datamol

Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify compl…

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. Enable molecular prop…

deepTools

deepTools is a comprehensive suite of Python command-line tools designed for processing and analy.

deepvariant

deepvariant.

Denario

Denario is a multiagent AI system designed to automate scientific research workflows from initial data analysis through publication-ready ma…

depmap

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

dhdna-profiler

A structured system for extracting the cognitive fingerprint of any text's author. Based on the Digital Human DNA (DHDNA) framework — the th…

DiffDock

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

differentiation-schemes

Select and apply numerical differentiation schemes for PDE/ODE discretization. Use when choosing finite difference/volume/spectral schemes,…

digital-twin-clinical-agent

Create patient digital twins for treatment simulation and outcome prediction.

DNAnexus Integration

DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, a…

docx

A.docx file is a.

docx

A user may ask you to create, edit, or analy.

drug-discovery-search

End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.

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 drug targets. This skil…

drugbank-search

Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu.

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 metadata. Access and…

Ensembl

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

epigenomics-methylgpt-agent

Epigenomics and DNA methylation analysis with MethylGPT-inspired approaches.

equity-scorer

Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity S…

esm

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

etetoolkit

ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analy.

exosome-ev-analysis-agent

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

Exploratory Data Analysis

Perform comprehensive exploratory data analysis (EDA) on scientific data files across multiple domains. This skill provides automated file t…

fastq-analysis-pipeline

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

fda-database

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

fhir-developer-skill

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

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 there a skill that can…

FluidSim

FluidSim is an object-oriented Python framework for high-performance computational fluid dynamics (CFD) simulations. It provides solvers for…

foldseek

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

FRED Economic Data

Access comprehensive economic data through FRED (Federal Reserve Economic Data), a database maintained by the Federal Reserve Bank of St. Lo…

galaxy-bridge

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

gatk-variant-calling

gatk-variant-calling.

gene-panel-design-agent

Design targeted gene panels for clinical or research sequencing applications.

Generate Image

Generate and edit high-quality images using OpenRouter's image generation models including FLUX.2 Pro and Gemini 3.1 Flash Image Preview.

geniml

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

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 genomics data. GEO contains…

geomaster

Comprehensive geospatial science skill covering GIS, remote sensing, spatial analysis, and ML for Earth observation across 70+ topics with 5…

GeoPandas

GeoPandas extends pandas to enable spatial operations on geometric types. It combines the capabilities of pandas and shapely for geospatial…

gget

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

Ginkgo Cloud Lab

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