smithery/gptomics

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bio-tcr-bcr-analysis-mixcr-analysis Align V(D)J reads and assemble TCR/BCR clonotypes with MiXCR, driven by a chemistry-matched preset. Use when choosing…

smithery/gptomics

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bio-tcr-bcr-analysis-repertoire-visualization Draws TCR/BCR repertoire figures - V-J chord/circos, CDR3 spectratype, clonal-space stratification, clonal tracking a…

smithery/gptomics

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bio-tcr-bcr-analysis-scirpy-analysis Integrates single-cell paired TCR/BCR (10x VDJ, AIRR, dandelion, BD Rhapsody) with gene expression in an AnnData/MuDa…

smithery/gptomics

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bio-tcr-bcr-analysis-vdjtools-analysis Computes immune-repertoire diversity, clonal structure, overlap, and segment usage from TCR/BCR clonotype tables with…

smithery/gptomics

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bio-transcription-translation Transcribe DNA to RNA and translate to protein using Biopython, with NCBI codon-table selection, CDS validation, and …

smithery/gptomics

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bio-uniprot-access Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross…

smithery/gptomics

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bio-variant-annotation Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools …

smithery/gptomics

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bio-variant-calling Call germline SNPs and indels from a BAM/CRAM with bcftools mpileup and call, and select the right calling engine for…

smithery/gptomics

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bio-variant-calling-clinical-interpretation Classify variant clinical significance with the ACMG/AMP germline framework and its 2018-2025 ClinGen refinements (gr…

smithery/gptomics

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bio-variant-calling-deepvariant Calls germline SNPs and indels with Google DeepVariant, which reframes variant calling as CNN image classification ov…

smithery/gptomics

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bio-variant-calling-filtering-best-practices Filters germline and somatic variant callsets at the site and genotype level with GATK VQSR (VQSLOD, truth-sensitivit…

smithery/gptomics

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bio-variant-calling-joint-calling Joint genotype a cohort of per-sample gVCFs with GATK (HaplotypeCaller -ERC GVCF -> GenomicsDBImport or CombineGVCFs …

smithery/gptomics

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bio-variant-calling-structural-variant-calling Call structural variants (>=50 bp deletions, insertions, inversions, duplications, translocations) from short- or lon…

smithery/gptomics

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bio-variant-normalization Left-align and trim indels to parsimonious canonical form, decompose MNPs (atomize), and split multiallelic variants …

smithery/gptomics

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bio-vcf-basics View, query, and interpret VCF/BCF variant files with bcftools and cyvcf2.

smithery/gptomics

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bio-vcf-manipulation Combine, split, sort, intersect, and subset VCF/BCF files with bcftools merge, concat, isec, sort, view, and reheader…

smithery/gptomics

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bio-vcf-statistics Compute and interpret VCF quality-control metrics (Ti/Tv, het/hom, novel/known, missingness, HWE, contamination, rela…

smithery/gptomics

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bio-workflow-management-nextflow-pipelines Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through cha…

smithery/gptomics

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bio-workflow-management-snakemake-workflows Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expa…

smithery/gptomics

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bio-workflow-management-wdl-workflows Authors bioinformatics pipelines in WDL (Workflow Description Language) run by Cromwell or miniwdl, targeting the GAT…

smithery/gptomics

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bio-workflows-atacseq-pipeline Orchestrates the end-to-end bulk ATAC-seq pipeline from FASTQ to differential accessibility and TF footprints, chaini…

smithery/gptomics

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bio-workflows-crispr-screen-pipeline End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, gui…

smithery/gptomics

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bio-workflows-cytometry-pipeline End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expresse…

smithery/gptomics

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bio-workflows-expression-to-pathways Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose…

smithery/gptomics

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bio-workflows-fastq-to-variants Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, ch…

smithery/gptomics

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bio-workflows-genome-assembly-pipeline Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rath…

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bio-workflows-gwas-pipeline Orchestrates the GWAS pipeline from genotypes to association results, chaining PLINK2 QC (variant-then-sample missing…

smithery/gptomics

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bio-workflows-hic-pipeline End-to-end Hi-C analysis workflow from FASTQ to compartments, TADs, and loops, with the decision of WHICH features th…

smithery/gptomics

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bio-workflows-imc-pipeline Orchestrates imaging mass cytometry from raw MCD acquisitions to patient-level spatial analysis, chaining steinbock p…

smithery/gptomics

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bio-workflows-longread-sv-pipeline Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matche…

smithery/gptomics

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bio-workflows-merip-pipeline Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene pl…

smithery/gptomics

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bio-workflows-metabolomics-pipeline Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalizati…

smithery/gptomics

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bio-workflows-metagenomics-pipeline End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host…

smithery/gptomics

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bio-workflows-microbiome-pipeline End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestra…

smithery/gptomics

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bio-workflows-multi-omics-pipeline Orchestrates VERTICAL bulk multi-omics integration (RNA + protein + methylation on the SAME samples) from harmonizati…

smithery/gptomics

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bio-workflows-multiome-pipeline Orchestrates the end-to-end 10x Multiome (paired scRNA + scATAC) pipeline from Cell Ranger ARC output to a jointly-em…

smithery/gptomics

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bio-workflows-proteomics-pipeline Orchestrates bottom-up proteomics from a search engine's output (MaxQuant/FragPipe/DIA-NN) to differential protein ab…

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bio-workflows-riboseq-pipeline End-to-end Ribo-seq analysis from FASTQ through periodicity QC, P-site calibration, ORF detection, translation effici…

smithery/gptomics

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bio-workflows-rnaseq-to-de Orchestrates the end-to-end bulk RNA-seq differential-expression pipeline from FASTQ to an annotated DE gene table, c…

smithery/gptomics

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bio-workflows-scrnaseq-pipeline Orchestrates the end-to-end single-cell RNA-seq pipeline from 10x Cell Ranger output to annotated cell types, chainin…

smithery/gptomics

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bio-workflows-smrna-pipeline Orchestrates the end-to-end small RNA-seq pipeline from FASTQ to differential miRNAs and expression-filtered targets,…

smithery/gptomics

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42

bio-workflows-somatic-variant-pipeline Chains a somatic (tumor-normal) SNV/indel and structural-variant pipeline end to end with GATK Mutect2 (or Strelka2),…

smithery/gptomics

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bio-workflows-spatial-pipeline Orchestrates the end-to-end spatial transcriptomics pipeline from Space Ranger / vendor output to spatial domains and…

smithery/gptomics

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bio-workflows-tcr-pipeline Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermuta…

smithery/gptomics

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

smithery/gptomics

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