345 skills · sorted by relevance
Search the European Nucleotide Archive for DNA and RNA sequences, raw sequencing reads, and assembled genomes. Retrieve records by accession, a unique record identifier, or filter by research metadata, then download data for analysis workflows.
Analyze genomic regions with gtars using Python or command-line tools. Find overlaps, generate coverage tracks showing read density, prepare regions as tokens for machine learning, and split single-cell fragment data for further analysis.
Look up how genetic differences affect medication response using ClinPGx. Retrieve gene–drug relationships, clinical guidelines, genetic variant functions, and drug labels to gather evidence for research and reviews of genotype-based dosing recommendations.
Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools, including planning-only questions.
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Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.
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Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.
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Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.
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Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.
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Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.
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Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
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Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
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Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.
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Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.
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Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.
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Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.
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Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.
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Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
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Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instruments, or running sensitivity analyses for causal inference.
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Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.
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Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
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Test whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc. Computes posterior probabilities for shared vs distinct causal variants between GWAS and eQTL signals. Use when determining if a GWAS signal and an eQTL share the same causal variant.
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Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
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This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.
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Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.
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