Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller.
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when performing joint genotyping across multiple samples.
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from short-read data.
Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. Use when a user has bulk count matrices and needs differential expression analysis in omicverse.
Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.
Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.
Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.
