smithery/gptomics

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bio-motif-search Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython an…

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bio-multi-omics-mixomics-analysis Builds supervised and unsupervised multivariate integration across bulk omics blocks with mixOmics - sPLS for sparse …

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bio-multi-omics-mofa-integration Discovers shared and view-specific latent factors across bulk multi-omics blocks (RNA-seq, proteomics, methylation) o…

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bio-multi-omics-similarity-network Stratifies patients into multi-omics subtypes by building one patient-by-patient similarity network per omic, fusing …

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bio-paired-end-fastq Handle paired-end FASTQ files (R1/R2) using Biopython while keeping mates synchronized. Use when working with Illumin…

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bio-pathway-go-enrichment Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hyp…

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bio-pathway-gsea Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterP…

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bio-pathway-kegg-pathways Tests gene lists, ranked vectors, and fold-change vectors against KEGG pathways and modules with clusterProfiler enri…

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bio-pathway-reactome Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-rev…

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bio-pathway-wikipathways Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pa…

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bio-phasing-imputation-genotype-imputation Imputes untyped genotypes against a phased reference panel with Beagle, Minimac4, or IMPUTE5 (array data) or from gen…

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bio-phasing-imputation-haplotype-phasing Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning…

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bio-phasing-imputation-imputation-qc Assesses and filters phasing/imputation output - the quality metrics (Beagle DR2, Minimac R2 and EmpRsq, IMPUTE/GLIMP…

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bio-phasing-imputation-reference-panels Selects and prepares the reference panel that phasing/imputation copies haplotypes from (1000 Genomes, HRC, TOPMed, H…

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bio-phylo-distance-calculations Build model-corrected evolutionary distance matrices and distance trees (NJ, BIONJ, FastME, UPGMA) with Biopython Bio…

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bio-phylo-modern-tree-inference Infers maximum-likelihood phylogenetic trees with IQ-TREE2 and RAxML-NG -- model selection (ModelFinder), branch supp…

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bio-phylo-tree-io Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser…

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bio-phylo-tree-manipulation Edit phylogenetic tree structure with Biopython Bio.Phylo, and treat rooting as a separate statistical inference rath…

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bio-phylo-tree-visualization Draw and export phylogenetic trees with Bio.Phylo plus matplotlib, and route rich figures to ggtree, ETE4, or iTOL. C…

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bio-pileup-generation Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant callin…

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bio-population-genetics-association-testing Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT…

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bio-population-genetics-linkage-disequilibrium Computes linkage disequilibrium (r2, D', composite Rogers-Huff r2), prunes correlated variants, clumps GWAS summary s…

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bio-population-genetics-plink-basics Manages PLINK genotype filesets - format conversion (VCF, BED/BIM/FAM, PED/MAP, pgen/pvar/psam) and sample/variant QC…

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bio-population-genetics-population-structure Infers and describes population structure with PCA (plink2 --pca, smartpca/EIGENSOFT, FlashPCA2), model-based cluster…

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bio-population-genetics-scikit-allel-analysis In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (p…

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bio-primer-design-primer-basics Designs and ranks PCR primer pairs for a target template with primer3-py (design_primers), returning pairs with neare…

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bio-primer-design-primer-validation Validates chosen PCR/qPCR oligos for intramolecular thermodynamic liabilities with primer3-py - hairpins, self-dimers…

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bio-primer-design-qpcr-primers Co-designs qPCR/RT-qPCR primers and hydrolysis (TaqMan) or molecular-beacon probes with primer3-py (PRIMER_PICK_INTER…

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bio-proteomics-data-import Loads mass-spectrometry data into Python/R and strips the search engine's bookkeeping before any number is trusted --…

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bio-proteomics-dia-analysis Analyzes data-independent acquisition (DIA) proteomics by scoring reconstructed fragment-chromatogram peak groups aga…

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bio-proteomics-differential-abundance Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqr…

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bio-proteomics-protein-inference Groups proteins from peptide identifications and controls protein-level FDR, framing inference as a chosen explanatio…

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bio-proteomics-proteomics-qc Quality control for bottom-up proteomics across three levels -- instrument/raw-signal (mass accuracy, RT/iRT fit, FWH…

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bio-proteomics-quantification Quantifies protein abundance from mass spectrometry using label-free (LFQ/MaxLFQ, DIA fragment-level), isobaric (TMT/…

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bio-proteomics-spectral-libraries Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relativ…

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bio-read-alignment-bowtie2-alignment Aligns DNA short reads to a reference with Bowtie2, choosing end-to-end (whole read must align) vs local (soft-clip r…

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bio-read-alignment-bwa-alignment Aligns DNA short reads (paired- or single-end) to a reference genome with bwa-mem2, the maintained successor to BWA-M…

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bio-read-alignment-hisat2-alignment Aligns RNA-seq reads to a genome with HISAT2, the splice-aware aligner whose hierarchical graph FM-index runs at roug…

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bio-read-alignment-star-alignment Aligns RNA-seq reads to a genome with STAR, the fast splice-aware aligner whose splice-junction database (built from …

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bio-read-qc-adapter-trimming Removes sequencing adapters from FASTQ reads with Cutadapt and Trimmomatic, including paired-end read-through, small-…

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bio-read-qc-contamination-screening Detects contamination in sequencing reads - cross-species (FastQ Screen, Kraken2), vector/PhiX/adapter, rRNA, and sam…

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bio-read-qc-fastp-workflow Runs all-in-one FASTQ preprocessing with fastp in a single pass - adapter trimming via paired-end overlap analysis, q…

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bio-read-qc-quality-reports Generates and interprets per-file and cross-sample QC reports from FASTQ data with FastQC, falco, and MultiQC, coveri…

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bio-read-qc-umi-processing Extracts UMIs and collapses reads to original molecules with umi_tools (directional dedup) or builds error-corrected …

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bio-read-sequences Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between str…

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bio-reference-operations Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, …

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bio-reporting-automated-qc-reports Aggregates per-tool QC metrics (FastQC, fastp, alignment, quantification, variant calling, single-cell) into one inte…

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bio-reporting-figure-export Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust p…

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bio-reporting-quarto-reports Builds reproducible Quarto reports, presentations, and websites across R, Python, and Julia, with correct engine sele…

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bio-reporting-rmarkdown-reports Creates reproducible R Markdown analysis reports (HTML, PDF, Word) with knitr, covering the render pipeline, the inte…

smithery/gptomics

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