Data & Analytics

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

1. Read the summary statistics file. 2. Identify genome-wide significant lead variants. 3. Compute the genomic inflation factor lambda. 4. Produce a QQ plot under `output/`. 5. Write a final summary JSON to `output/summary.json` with fields for lead count, lambda, and plot path.

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

Ancestry decomposition PCA against the Simons Genome Diversity Project

Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation. Exposes an MCP stdio server for live AI integration alongside a ClawBio CLI runner.

Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis

Detect Neanderthal and Denisovan introgression segments from modern human genomes

Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer,

Use this skill — NOT browser or web_fetch — for ALL Polymarket, Kalshi, Limitless, Opinion, Predict.Fun, dFlow, UMA oracle, and prediction market data. Provides structured API at localhost:8402/v1/pm/* for markets, cross-venue search, leaderboard, smart money, wallet analytics, wallet identity & clustering, UMA resolution status, and odds.

Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning.

Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.

Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting...

Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucleotide reactivity profiles that constrain structure prediction. Use when processing SHAPE-MaP or DMS-MaPseq sequencing data to obtain experimental RNA structure information.

Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

Statistical analysis for metabolomics data. Covers preprocessing (log2 transformation, normalization), limma moderated testing with empirical Bayes, Welch's t-tests with BH correction, fold change estimation, and multivariate methods (PCA, PLS-DA, OPLS-DA). Use when identifying differentially abundant metabolites or building classification models.

Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.

End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comp...

Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows gene tree discordance from incomplete lineage sorting, when in the anomaly zone where concatenation is misleading, or when computing concordance factors to assess topological support.

Delimits species boundaries from molecular data using distance-based (ASAP), tree-based (bPTP, GMYC), and coalescent (BPP) methods. Compares multiple delimitation results with delimtools. Use when delineating putative species from DNA barcoding data, resolving cryptic species complexes, or validating taxonomic assignments. Emphasizes multi-method consensus following integrative taxonomy best practice.

End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy. Use when analyzing spatial transcriptomics data.

Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.

End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer genomics. Use when calling somatic mutations from tumor-normal pairs.