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1. ▌
   Claude Agent System Instructions 3 · tools-only bundle

   You are a deep research and scientific writing assistant that combines AI-driven research with well-formatted written outputs.
   7 repo stars
2. ▌
   Claude Agent System Instructions 4 · tools-only bundle

   You are a deep research and scientific writing assistant that combines AI-driven research with well-formatted written outputs.
   7 repo stars
3. ▌
   Asset Patterns Reference · tools-only bundle

   Once you've defined assets, use the dg launch command to materialize them. For comprehensive documentation on launching assets, see the CLI launch reference.
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4. ▌
   Asset Patterns Reference 2 · tools-only bundle

   Once you've defined assets, you'll need to materialize (launch) them. Use the modern dg launch command for all asset execution.
   7 repo stars
5. ▌
   Intelligent Scaffolding · tools-only bundle

   I'll create complete feature structures based on your project patterns, with full continuity across sessions.
   7 repo stars
6. ▌
   Integration Scaffolding · tools-only bundle

   Invoke the /dagster-integrations skill to help find an existing integration component that matches the user's use case.
   7 repo stars
7. ▌
   Exceptions Module · tools-only bundle

   Defines a custom exception hierarchy for structured error handling throughout TunaCode.
   7 repo stars
8. ▌
   Kraken2 Classification Usage Guide · tools-only bundle

   Kraken2 is a fast taxonomic classifier that uses exact k-mer matches to assign reads to taxonomic nodes. It's highly accurate for well-represented taxa and ideal for screening large datasets.
   7 repo stars
9. ▌
   Cross Validation Usage Guide · tools-only bundle

   Implement proper cross-validation strategies to get unbiased performance estimates on biomedical datasets and avoid overfitting during biomarker discovery.
   7 repo stars
10. ▌
    Figure Export Usage Guide · tools-only bundle

    This guide covers exporting publication-ready figures with proper resolution, sizing, and formatting.
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11. ▌
    Functional Prediction Usage Guide · tools-only bundle

    PICRUSt2 predicts metagenome functional content from 16S/18S marker gene data by inferring gene content from phylogenetically related reference genomes.
    7 repo stars
12. ▌
    Local Blast Usage Guide · tools-only bundle

    This skill enables AI agents to help you run BLAST searches locally using BLAST+ command-line tools, enabling fast unlimited searches against custom or downloaded databases.
    7 repo stars
13. ▌
    Fcs Handling Usage Guide · tools-only bundle

    FCS (Flow Cytometry Standard) is the standard file format for cytometry data. flowCore provides comprehensive tools for reading, writing, and manipulating FCS files.
    7 repo stars
14. ▌
    Bowtie2 Alignment Usage Guide · tools-only bundle

    Bowtie2 is a fast and memory-efficient aligner for short reads. It supports both end-to-end and local alignment modes, making it versatile for ChIP-seq, ATAC-seq, and general short-read alignment.
    7 repo stars
15. ▌
    Mageck Analysis Usage Guide · tools-only bundle

    MAGeCK is the standard tool for analyzing pooled CRISPR screens. It handles count normalization, identifies significantly enriched/depleted genes, and performs pathway analysis.
    7 repo stars
16. ▌
    Hit Calling Usage Guide · tools-only bundle

    Multiple methods exist for calling hits in CRISPR screens. The choice depends on screen design, reference data availability, and desired stringency.
    7 repo stars
17. ▌
    Vcf Manipulation Usage Guide · tools-only bundle

    This guide covers merging, concatenating, sorting, and comparing VCF files.
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18. ▌
    Mirdeep2 Analysis Usage Guide · tools-only bundle

    Discover novel miRNAs and quantify known miRNAs using miRDeep2's de novo prediction algorithm based on secondary structure and read patterns.
    7 repo stars
19. ▌
    Star Rna Seq Alignment Usage Guide · tools-only bundle

    STAR (Spliced Transcripts Alignment to a Reference) is the most widely used RNA-seq aligner. It's extremely fast, supports splice-aware alignment, and can detect novel junctions with two-pass mode.
    7 repo stars
20. ▌
    Pileup Generation Usage Guide · tools-only bundle

    Generate pileup data showing all reads covering each genomic position for variant calling and position-level analysis.
    7 repo stars
21. ▌
    Taxonomy Assignment Usage Guide · tools-only bundle

    Taxonomic assignment classifies ASVs or OTUs to taxonomic ranks (Kingdom through Species) using reference databases like SILVA, GTDB, or UNITE.
    7 repo stars
22. ▌
    Proximity Operations Usage Guide · tools-only bundle

    Proximity operations help you find relationships between genomic features based on their distance.
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23. ▌
    Iso Seq Analysis Usage Guide · tools-only bundle

    Process PacBio Iso-Seq data for full-length transcript discovery and isoform characterization.
    7 repo stars
24. ▌
    Genotype Imputation Usage Guide · tools-only bundle

    Genotype imputation predicts untyped variants using haplotype patterns from a reference panel, enabling increased variant density for GWAS, fine-mapping, and polygenic risk score calculation.
    7 repo stars
25. ▌
    Alerting Integrations · tools-only bundle

    Notification and alerting systems for pipeline monitoring, team communication, and incident management.
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26. ▌
    Alerting Webhooks · tools-only bundle

    import Image from '@theme/IdealImage'; import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem';
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27. ▌
    Alerting API Reference · tools-only bundle

    Complete reference for Grafana Alerting HTTP API endpoints (Grafana 9.0+).
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28. ▌
    Decision Checklists Reference · tools-only bundle

    If any answer is "yes", wrap in a @cache-decorated function instead.
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29. ▌
    Type Annotations Python 3 11 · tools-only bundle

    This document provides complete, canonical type annotation guidance for Python 3.11.
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30. ▌
    Type Annotations Python 3 13 · tools-only bundle

    This document provides complete, canonical type annotation guidance for Python 3.13. Python 3.13 implements PEP 649 (Deferred Evaluation of Annotations), fundamentally changing how annotations are evaluated.
    7 repo stars
31. ▌
    API Design Reference · tools-only bundle

    boilerplate are explicitly exempt. These helpers often wrap complex constructors (like formatplanheader_body) with sensible defaults, and having many default parameters is their intended purpose—not a code smell
    7 repo stars
32. ▌
    MCP Overview 4 · tools-only bundle

    import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; import Image from '@theme/IdealImage';
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33. ▌
    Ribosome Stalling Usage Guide · tools-only bundle

    Detect ribosome pausing and stalling sites at codon resolution to study translational regulation, rare codon effects, and nascent chain interactions.
    7 repo stars
34. ▌
    Type Annotations Python 3 12 · tools-only bundle

    This document provides complete, canonical type annotation guidance for Python 3.12.
    7 repo stars
35. ▌
    Figlet Text Converter Usage Guide · tools-only bundle

    The Figlet Text Converter skill converts marked text in files to ASCII art. It uses a universal tag syntax that works across all file types and intelligently preserves comment formatting.
    7 repo stars
36. ▌
    Entrez Link Usage Guide · tools-only bundle

    This skill enables AI agents to help you navigate between NCBI databases, finding related records across different data types (genes, proteins, sequences, publications).
    7 repo stars
37. ▌
    Atac Seq Peak Calling Usage Guide · tools-only bundle

    Call accessible chromatin regions from ATAC-seq data using MACS3 or Genrich, with specialized handling for Tn5 transposase cut sites and nucleosome-free region detection.
    7 repo stars
38. ▌
    Structure Navigation Usage Guide · tools-only bundle

    This skill covers navigating the SMCRA (Structure-Model-Chain-Residue-Atom) hierarchy in Biopython Bio.PDB.
    7 repo stars
39. ▌
    Functional Profiling Usage Guide · tools-only bundle

    HUMAnN3 profiles the functional potential of metagenomic communities by quantifying gene families (UniRef90) and inferring pathway abundances (MetaCyc).
    7 repo stars
40. ▌
    Pairwise Alignment Usage Guide · tools-only bundle

    This skill performs pairwise sequence alignment to compare two DNA, RNA, or protein sequences. It uses Biopython's PairwiseAligner class which implements dynamic programming algorithms for finding optimal alignments.
    7 repo stars
41. ▌
    Lineage Tracing Analysis Usage Guide · tools-only bundle

    Reconstruct cell lineage trees from CRISPR barcodes, mitochondrial mutations, or other heritable markers.
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42. ▌
    Chip Seq Qc Usage Guide · tools-only bundle

    Quality control metrics for ChIP-seq experiments including FRiP, NSC/RSC, IDR, and library complexity measurements to assess enrichment quality and replicate reproducibility.
    7 repo stars
43. ▌
    Dg Scaffold Create Definitions · tools-only bundle

    Scaffold Dagster definitions including Python objects (assets, schedules, sensors) and integration components.
    7 repo stars
44. ▌
    Dg Scaffold Create Definitions 2 · tools-only bundle

    Scaffold Dagster definitions including Python objects (assets, schedules, sensors) and integration components.
    7 repo stars
45. ▌
    Alignment Indexing Usage Guide · tools-only bundle

    Create and use indices for random access to BAM and CRAM files, enabling fast region queries without reading entire files.
    7 repo stars
46. ▌
    Qpcr Primer And Probe Design Usage Guide · tools-only bundle

    This skill covers designing primers and probes for quantitative PCR (real-time PCR) using primer3-py. Supports TaqMan hydrolysis probes and SYBR Green primer-only assays.
    7 repo stars
47. ▌
    Adapter Trimming Usage Guide · tools-only bundle

    Sequencing adapters must be removed before alignment to prevent misalignment and artifacts.
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48. ▌
    Hisat2 Rna Seq Alignment Usage Guide · tools-only bundle

    HISAT2 is a memory-efficient splice-aware aligner for RNA-seq data. It uses a graph-based index that enables fast alignment with low memory usage (~8GB for human genome vs ~30GB for STAR).
    7 repo stars
49. ▌
    Differential Splicing Usage Guide · tools-only bundle

    Detect differential alternative splicing between experimental conditions. Identifies splicing events that change significantly between groups, reporting both statistical significance and effect size (delta PSI).
    7 repo stars
50. ▌
    Mofa2 Integration Usage Guide · tools-only bundle

    MOFA2 (Multi-Omics Factor Analysis v2) is an unsupervised method for integrating multiple omics layers. It decomposes the data into latent factors that explain shared and view-specific variation.
    7 repo stars
51. ▌
    Heatmaps And Clustering Usage Guide · tools-only bundle

    Clustered heatmaps visualize matrix data (expression, methylation, etc.) with hierarchical clustering to reveal patterns across samples and features.
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52. ▌
    Atac Seq Qc Usage Guide · tools-only bundle

    Assess ATAC-seq library quality using TSS enrichment, FRiP scores, fragment size distributions, mitochondrial contamination, and library complexity metrics.
    7 repo stars
53. ▌
    Pathway Mapping Usage Guide · tools-only bundle

    Pathway mapping places differential metabolites in biological context, identifying affected metabolic processes using enrichment analysis and pathway topology.
    7 repo stars
54. ▌
    Classification Models Usage Guide · tools-only bundle

    Build classification models for biomarker discovery and diagnostics using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs.
    7 repo stars
55. ▌
    Entrez Search Usage Guide · tools-only bundle

    This skill enables AI agents to help you search NCBI databases using Biopython's Entrez module. It covers keyword searches, database exploration, and query building.
    7 repo stars
56. ▌
    Card Format · tools-only bundle

    Bugs, docs, and module cards all use this unified structure.
    7 repo stars
57. ▌
    Scenic Regulons Usage Guide · tools-only bundle

    Infer transcription factor regulons from single-cell RNA-seq data using the pySCENIC three-step pipeline.
    7 repo stars
58. ▌
    Sashimi Plots Usage Guide · tools-only bundle

    Create sashimi plots to visualize splicing events with read coverage and splice junction counts.
    7 repo stars
59. ▌
    Sparse Matrix Handling Usage Guide · tools-only bundle

    Work with sparse matrices (CSR, CSC, COO) for memory-efficient storage and operations on count data with many zero values, especially single-cell RNA-seq data.
    7 repo stars
60. ▌
    Repertoire Visualization Usage Guide · tools-only bundle

    Create publication-quality visualizations of immune repertoire data including V-J circos plots, clone tracking, diversity comparisons, and clonotype networks.
    7 repo stars
61. ▌
    Metagenome Visualization Usage Guide · tools-only bundle

    Visualize and statistically analyze metagenomic profiles using Python (matplotlib, seaborn, scikit-learn) or R (phyloseq, vegan, ggplot2).
    7 repo stars
62. ▌
    Targeted Metabolomics Usage Guide · tools-only bundle

    Targeted metabolomics quantifies a predefined set of metabolites using selected reaction monitoring (SRM/MRM). This approach provides absolute quantification with high sensitivity and reproducibility.
    7 repo stars
63. ▌
    Secondary Structure Prediction Usage Guide · tools-only bundle

    Predict RNA secondary structures from sequence using thermodynamic models. ViennaRNA computes minimum free energy (MFE) structures, partition function ensembles, base-pair probabilities, consensus structures from…
    7 repo stars
64. ▌
    Interaction Databases Usage Guide · tools-only bundle

    This skill enables AI agents to query protein-protein interaction (PPI) databases including STRING, BioGRID, IntAct, and OmniPath.
    7 repo stars
65. ▌
    Upset Plots Usage Guide · tools-only bundle

    UpSet plots visualize set intersections more effectively than Venn diagrams, especially for 4+ sets. They show intersection sizes as bar charts with a matrix indicating which sets participate.
    7 repo stars
66. ▌
    Time Series De Usage Guide · tools-only bundle

    Identify genes with significant temporal expression patterns across time-course experiments using spline models, polynomial regression, or likelihood ratio tests.
    7 repo stars
67. ▌
    Multiomics Grn Inference Usage Guide · tools-only bundle

    Build enhancer-driven gene regulatory networks by integrating single-cell RNA-seq and ATAC-seq data.
    7 repo stars
68. ▌
    Alignment Statistics Usage Guide · tools-only bundle

    Generate QC statistics from alignment files including mapping rates, read counts, coverage depth, and per-chromosome distributions.
    7 repo stars
69. ▌
    Quarto Reports Usage Guide · tools-only bundle

    Quarto is a next-generation scientific publishing system supporting R, Python, Julia, and Observable with enhanced features over R Markdown.
    7 repo stars
70. ▌
    Uniprot Access Usage Guide · tools-only bundle

    This skill enables AI agents to help you query UniProt programmatically using the REST API to retrieve protein sequences, annotations, and functional information.
    7 repo stars
71. ▌
    Dbsnp Queries Usage Guide · tools-only bundle

    Query dbSNP for rsID lookups, coordinate mapping, and variant annotations using myvariant.info or NCBI Entrez APIs.
    7 repo stars
72. ▌
    Cnv Annotation Usage Guide · tools-only bundle

    CNV annotation adds biological context to copy number calls by identifying affected genes, pathways, and clinical significance. This is essential for interpreting CNV findings in research and clinical contexts.
    7 repo stars
73. ▌
    Scaffolding Usage Guide · tools-only bundle

    Scaffolding orders and orients contigs into chromosome-level assemblies using Hi-C proximity ligation data to infer long-range contacts.
    7 repo stars
74. ▌
    Flow Cytometry Pipeline Usage Guide · tools-only bundle

    This workflow processes flow cytometry data from raw FCS files through compensation, transformation, clustering or gating, and differential analysis.
    7 repo stars
75. ▌
    Ggplot2 Fundamentals Usage Guide · tools-only bundle

    ggplot2 is a declarative visualization system based on the Grammar of Graphics. Build publication-quality figures layer by layer.
    7 repo stars
76. ▌
    Conservation Genetics Usage Guide · tools-only bundle

    Assesses the genetic health of populations for conservation management. Covers F-statistics and genetic diversity metrics (hierfstat), allelic richness, pairwise population differentiation, runs of homozygosity for…
    7 repo stars
77. ▌
    Circadian Rhythm Detection Usage Guide · tools-only bundle

    Detects circadian and ultradian rhythms in time-series omics data. Fits cosinor regression models to estimate rhythm parameters (amplitude, phase, MESOR) and applies non-parametric tests (JTK_CYCLE, RAIN) to identify…
    7 repo stars
78. ▌
    Hi C Visualization Usage Guide · tools-only bundle

    This skill covers visualizing Hi-C contact matrices, TADs, loops, and other genomic features using matplotlib, cooltools, and HiCExplorer.
    7 repo stars
79. ▌
    Population Structure Usage Guide · tools-only bundle

    Population structure analysis identifies genetic ancestry and stratification using PCA (continuous clustering) and ADMIXTURE (discrete ancestry proportions).
    7 repo stars
80. ▌
    Time Series De Usage Guide 2 · tools-only bundle

    Identify genes with significant temporal expression patterns across time-course experiments using spline models, polynomial regression, or likelihood ratio tests.
    7 repo stars
81. ▌
    Co Expression Networks Usage Guide · tools-only bundle

    Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes.
    7 repo stars
82. ▌
    Structure Modification Usage Guide · tools-only bundle

    This skill covers modifying protein structures: transforming coordinates, removing/adding atoms and residues, modifying B-factors and occupancies, and building structures programmatically.
    7 repo stars
83. ▌
    Splicing Pipeline Usage Guide · tools-only bundle

    Complete alternative splicing analysis workflow from raw RNA-seq FASTQ files to differential splicing results and visualizations. Includes QC checkpoints and best practices.
    7 repo stars
84. ▌
    Network Visualization Usage Guide · tools-only bundle

    This skill enables AI agents to create static, interactive, and publication-quality visualizations of biological networks.
    7 repo stars
85. ▌
    Vcf Statistics Usage Guide · tools-only bundle

    This guide covers generating variant statistics and quality metrics.
    7 repo stars
86. ▌
    Single Cell Preprocessing Usage Guide · tools-only bundle

    This skill covers quality control, filtering, and normalization for single-cell RNA-seq data using both Seurat (R) and Scanpy (Python). These are essential steps before clustering and downstream analysis.
    7 repo stars
87. ▌
    Spectral Libraries Usage Guide · tools-only bundle

    Build and use spectral libraries containing reference MS2 spectra for faster and more sensitive peptide identification in DIA and targeted proteomics.
    7 repo stars
88. ▌
    Nucleosome Positioning Usage Guide · tools-only bundle

    Extract nucleosome positions from ATAC-seq fragment size patterns using ATACseqQC or NucleoATAC to understand chromatin structure at promoters and regulatory regions.
    7 repo stars
89. ▌
    Co Expression Networks Usage Guide 2 · tools-only bundle

    Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes.
    7 repo stars
90. ▌
    Tumor Fraction Estimation Usage Guide · tools-only bundle

    Estimate circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations and calculates ctDNA percentage for treatment monitoring.
    7 repo stars
91. ▌
    Wikipathways Enrichment Usage Guide · tools-only bundle

    WikiPathways is an open, collaborative platform for biological pathways with CC0 license, community curation, and support for 30+ species including many not covered by KEGG or Reactome.
    7 repo stars
92. ▌
    Alignment Validation Usage Guide · tools-only bundle

    Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics before downstream analysis.
    7 repo stars
93. ▌
    Super Enhancers Usage Guide · tools-only bundle

    Identify super-enhancers from H3K27ac ChIP-seq data using ROSE or HOMER. Super-enhancers are large clusters of enhancers that control cell identity genes and are often altered in cancer.
    7 repo stars
94. ▌
    Neoantigen Pipeline Usage Guide · tools-only bundle

    This workflow identifies tumor-specific neoantigens from somatic mutations for personalized cancer vaccine design.
    7 repo stars
95. ▌
    Diversity Analysis Usage Guide 2 · tools-only bundle

    Diversity analysis characterizes microbial community structure through alpha (within-sample) and beta (between-sample) diversity metrics using phyloseq and vegan.
    7 repo stars
96. ▌
    De Visualization Usage Guide · tools-only bundle

    This skill covers creating publication-quality visualizations for differential expression results, including MA plots, volcano plots, PCA plots, and heatmaps. Works with both DESeq2 and edgeR output.
    7 repo stars
97. ▌
    Clustering And Phenotyping Usage Guide · tools-only bundle

    Unsupervised clustering identifies cell populations without predefined gates. Useful for discovery and high-dimensional CyTOF/spectral flow data.
    7 repo stars
98. ▌
    Enrichment Visualization Usage Guide · tools-only bundle

    The enrichplot package provides visualization functions for clusterProfiler results, including dot plots, bar plots, networks, and GSEA-specific plots.
    7 repo stars
99. ▌
    Differential Abundance Usage Guide · tools-only bundle

    Differential abundance testing identifies taxa that differ significantly between experimental groups while accounting for the compositional nature of microbiome data.
    7 repo stars
100. ▌
     Species Delimitation Usage Guide · tools-only bundle

     Delimits putative species boundaries from molecular data using complementary approaches: distance-based partitioning (ASAP), tree-based branching rate models (bPTP, GMYC), and full coalescent analysis (BPP).
     7 repo stars