Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.

Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.

Two-sample Mendelian Randomisation from GWAS summary statistics with IVW, MR-Egger, weighted median/mode, and full sensitivity analysis (Cochran Q, Egger intercept, Steiger, F-statistic, leave-one-out).

Render a 4-panel regional LocusCompare diagnostic for one (lead variant, exposure study, outcome study) tuple - overlays GWAS Manhattan, QTL Manhattan, GENCODE gene track, and cross-trait scatter colored by LD r². Use when an agent needs visual confirmation that two GWAS / QTL signals share the same causal variant (the Liu 2019 LocusCompare convention). Inputs: lead variant + two pre-fetched harmonised sumstats slices (or eQTL Catalogue / GWAS Catalog identifiers for bundled fetch). Output: PNG + JSON manifest.

Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle.

Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified. Use when an agent needs LD coloring for a regional plot or LD pruning around a candidate causal variant. Single client (on-demand region fetch from EBI 1000G FTP); no multi-GB cold-start.

Query and display Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy. Supports offline demo mode with synthetic biology data.

Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.

HLA allele typing from WGS/WES VCF data

End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing. Produces Manhattan plots, QQ plots, clumped lead variants, and structured summary statistics.

Predict tissue / cell-type expression (log TPM + TPM) from a 9,198 bp TSS-centered DNA sequence using the Genomic Intelligence G0 Expression model, via the hosted /v1/tasks/expression/predict API. The model is conditioned on a free-text cell-type / assay description.

Predict gene and transcript structure (intervals, exons, strand) from a DNA sequence using the Genomic Intelligence DNA Annotation model, via the hosted /v1/tasks/annotation/predict API. Async-only — the pipeline takes ~20 s for ~20 kbp.

Score genetic compatibility across all male-female pairings in a Genomebook generation

Flow.bio API bridge — authenticate, browse pipelines/samples/projects, search, upload data, launch pipeline executions, and check run status on any Flow instance.

Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).

Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset (study × tissue × quantification method). Input: dataset_id, chromosome, start, end, optional molecular_trait_id. Output: harmonised TSV slice.

Objective-driven pooled viability screen analysis: QC, hit calling, context-selectivity, biomarker sweep, and ranked repurposing candidates. Format-agnostic via schema.yaml + objective.yaml; includes offline demo.

Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance

Full reimplementation of DnaSP 6 for population genetics analysis of aligned DNA sequences. Covers nucleotide diversity, haplotype statistics, neutrality tests (Tajima's D, Fu & Li's D*/F*, R2), linkage disequilibrium (D, D', R², ZnS, Za, ZZ), minimum recombination (Rm), mismatch distribution, InDel polymorphism, between-population divergence (Dxy, Da, fixed/shared sites), outgroup-based Fu & Li D/F tests (fuliout), the HKA multi-locus neutrality test (hka), the McDonald-Kreitman test (mk), Ka/Ks (dN/dS) via the Nei-Gojobori (1986) method (kaks), Fu's Fs test (fufs), the site frequency spectrum (sfs, folded and outgroup-unfolded), transition/transversion ratio (tstv), and codon usage bias - RSCU (Sharp & Li 1987) and ENC (Wright 1990) (codon). Accepts FASTA or NEXUS input; outputs DnaSP-compatible TSV and a Markdown report.

Summarise pre-computed differential expression results with ranked gene lists, biological themes, and publication-ready interpretation.