← all plugins

1. ▌
   dnasp · gabrielmoreira bundle

   Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.
   17
   repo stars
2. ▌
   clinpgx · gabrielmoreira bundle

   Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels.
   17
   repo stars
3. ▌
   labstep · gabrielmoreira bundle

   Queries and displays Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy, with an offline demo mode using synthetic biology data.
   17
   repo stars
4. ▌
   nutrigx · gabrielmoreira bundle

   Generates a personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) by interrogating nutritionally-relevant SNPs and producing actionable dietary guidance, all computed locally.
   17
   repo stars
5. ▌
   wgs-prs · gabrielmoreira bundle

   Takes raw whole-genome sequencing FASTQ files or a pre-existing VCF through variant calling, quality control, and polygenic risk score computation using the PGS Catalog.
   17
   repo stars
6. ▌
   bgpt-mcp · gabrielmoreira bundle

   Search scientific papers via the BGPT MCP server and retrieve structured experimental data — methods, results, conclusions, quality scores, and 25+ metadata fields per paper.
   17
   repo stars
7. ▌
   fastreer · gabrielmoreira bundle

   Computes phylogenetic distance matrices and trees from genomic VCF or FASTA data using the fastreeR hybrid Java/Python toolkit.
   17
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8. ▌
   flow-bio · gabrielmoreira bundle

   Authenticate, browse pipelines, samples, and projects, upload data, launch pipeline executions, and check run status on any Flow.bio instance via CLI.
   17
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9. ▌
   gwas-prs · gabrielmoreira bundle

   Calculate polygenic risk scores from direct-to-consumer genetic data using published scoring files from the PGS Catalog and contextualize results against population reference distributions.
   17
   repo stars
10. ▌
    soul2dna · gabrielmoreira bundle

    Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mapping.
    17
    repo stars
11. ▌
    bioqc-mcp · gabrielmoreira bundle

    Automates sequencing quality control by running FastQC and MultiQC, extracting quality metrics, and generating publication-ready visualizations via a CLI or MCP stdio server.
    17
    repo stars
12. ▌
    gi-splice · gabrielmoreira bundle

    Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.
    17
    repo stars
13. ▌
    rnaseq-de · gabrielmoreira bundle

    Performs differential expression analysis on bulk RNA-seq or pseudo-bulk count matrices with QC, PCA, and contrast testing.
    17
    repo stars
14. ▌
    de-summary · gabrielmoreira

    Takes pre-computed differential expression results from DESeq2, edgeR, limma, or PyDESeq2 and produces a structured, publication-ready summary with ranked gene lists, biological themes, and key observations.
    17
    repo stars
15. ▌
    drug-photo · gabrielmoreira bundle

    Identifies a medication from a photo and generates a genotype-informed dosage card using CPIC guidelines and real 23andMe data.
    17
    repo stars
16. ▌
    hla-typing · gabrielmoreira bundle

    Performs HLA allele genotyping from WGS/WES VCF data, producing a structured markdown report and machine-readable JSON results.
    17
    repo stars
17. ▌
    polars-bio · gabrielmoreira bundle

    Perform fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames via the polars-bio library, serving as a scalable alternative to bioframe and bedtools.
    17
    repo stars
18. ▌
    gi-enhancer · gabrielmoreira bundle

    Predicts enhancer activity in DNA sequences using the hosted Genomic Intelligence G0 DeepSTARR model, returning per-window activity scores.
    17
    repo stars
19. ▌
    gi-promoter · gabrielmoreira bundle

    Detect promoter regions in DNA sequences by calling the Genomic Intelligence G0 transformer (GENA-LM BERT Large) hosted API. Returns per-window promoter probabilities and called regions as a report and JSON, from a single FASTA input.
    17
    repo stars
20. ▌
    gwas-lookup · gabrielmoreira bundle

    Queries 9 genomic databases in parallel for a given rsID, returning unified GWAS, PheWAS, eQTL, and fine-mapping reports.
    17
    repo stars
21. ▌
    fine-mapping · gabrielmoreira bundle

    Statistical fine-mapping of GWAS loci using SuSiE, SuSiE-inf, and Approximate Bayes Factors to identify credible sets and posterior inclusion probabilities (PIPs) for causal variant discovery. SuSiE-inf adds an infinitesimal polygenic component for improved calibration at well-powered loci.
    17
    repo stars
22. ▌
    genome-match · gabrielmoreira bundle

    Scores genetic compatibility between all male-female pairings in a Genomebook generation, ranking optimal mating pairs based on heterozygosity, trait complementarity, and disease risk.
    17
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23. ▌
    gi-chromatin · gabrielmoreira bundle

    Predicts chromatin state across 919 tracks (histone marks, DNase, TF binding) for DNA sequences via the hosted Genomic Intelligence API, producing a report and JSON results.
    17
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24. ▌
    just-prs-mcp · gabrielmoreira bundle

    Computes evidence-aware polygenic risk scores from local VCF or WGS files using the just-prs engine and a pinned local MCP server, with honest interpretation and model comparison.
    17
    repo stars
25. ▌
    protocols-io · gabrielmoreira bundle

    Search, browse, and retrieve scientific protocols from protocols.io via REST API, including private protocols with client token authentication.
    17
    repo stars
26. ▌
    recombinator · gabrielmoreira bundle

    Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.
    17
    repo stars
27. ▌
    seq-wrangler · gabrielmoreira bundle

    Runs NGS read QC, alignment, and BAM processing, wrapping FastQC, BWA/Bowtie2/Minimap2, SAMtools, and MultiQC for automated read-to-BAM workflows.
    17
    repo stars
28. ▌
    analyze-fasta · gabrielmoreira bundle

    Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.
    17
    repo stars
29. ▌
    equity-scorer · gabrielmoreira bundle

    Computes HEIM diversity and equity metrics from VCF or ancestry data, generating heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.
    17
    repo stars
30. ▌
    galaxy-bridge · gabrielmoreira bundle

    Discovers and executes bioinformatics tools from the Galaxy ecosystem via natural language, with multi-signal scoring, workflow templates, and reproducibility bundles.
    17
    repo stars
31. ▌
    gi-annotation · gabrielmoreira bundle

    Predicts gene and transcript structure from a DNA sequence using the hosted Genomic Intelligence API, producing a report and JSON output.
    17
    repo stars
32. ▌
    gi-expression · gabrielmoreira bundle

    Predicts tissue or cell-type gene expression (log TPM and TPM) from a TSS-centered DNA sequence using the hosted Genomic Intelligence G0 Expression model, conditioned on a free-text cell-type description.
    17
    repo stars
33. ▌
    gwas-pipeline · gabrielmoreira bundle

    Automates genome-wide association studies from genotype files to publication-ready results, running PLINK2 QC and REGENIE regression with Manhattan and QQ plots.
    17
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34. ▌
    ncbi-datasets · gabrielmoreira bundle

    Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
    17
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35. ▌
    proteomics-de · gabrielmoreira bundle

    Performs differential expression analysis on label-free quantitative (LFQ) proteomics data from MaxQuant and DIA-NN outputs, including preprocessing, imputation, statistical testing, and visualization.
    17
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36. ▌
    skill-builder · gabrielmoreira bundle

    Scaffolds a new ClawBio skill from a JSON/YAML spec or interactively, generating SKILL.md, Python skeleton, tests, and updating the catalog.
    17
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37. ▌
    ukb-navigator · gabrielmoreira bundle

    Searches UK Biobank's 12,000+ data fields and publications by natural language query, returning ranked field IDs and descriptions for research questions.
    17
    repo stars
38. ▌
    vcf-annotator · gabrielmoreira bundle

    Annotates VCF variants using Ensembl VEP, ClinVar, and gnomAD, ranks them by predicted impact, and generates a reproducible report.
    17
    repo stars
39. ▌
    busco-assessor · gabrielmoreira bundle

    Assesses genome, transcriptome, and protein completeness with BUSCO v6, automatically resolving the correct lineage from an organism description and generating reproducible reports.
    17
    repo stars