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Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-...
Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation pattern...
Generate Baujat plots for heterogeneity analysis. Identify studies that contribute most to the overall meta-analysis results and heterogeneity, helping discover potential outlier studies. Input meta-analysis data CSV, output Baujat plot PNG and contribution data CSV.
Generate meta-analysis forest plots for binary classification data. Input is a CSV file containing study names, event counts and sample sizes for experimental and control groups. Output includes forest plot PNG and data table CSV.
Generate Meta-analysis funnel plots and perform publication bias testing. Takes CSV file with Meta-analysis data as input, outputs funnel plot PNG, Egger test and Begg test results.
Generate radial plots (Radial Plot/Galbraith Plot) for heterogeneity analysis. Visually assess heterogeneity across studies by displaying the relationship between standardized effect sizes and precision. Input: Meta-analysis data in CSV format; Output: Radial plot PNG and data CSV.
Generate publication-quality sequence logos for DNA or protein motifs.
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.
Analyze data with `pseudotime-trajectory-viz` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.
Kaplan-Meier survival analysis tool for clinical and biological research. Generates publication-ready survival curves with statistical tests.
Search for gene expression DataSets and Profiles in the NCBI GEO database. Use this skill when the user wants to find microarray, RNA-seq, or other genomic data by keywords, organism, author, or specific fields.
Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).
Score the novelty of biological targets through literature mining and.
Generate Circos configuration files for circular genomics data visualization. Supports genomic variations (SNPs, CNVs, structural variants), cell-cell communication networks, and custom track configurations for publication-ready circular plots.
Automated generation of baseline characteristics tables (Table 1) for clinical research papers.
Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismark_methylation_extractor (Bismark BAM) or the aligner-agnostic MethylDackel/BISCUIT (bwa-meth BAM), producing the beta value M/(M+U) as a coverage file, bedGraph, or genome-wide cytosine report across CpG/CHG/CH...
Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across sample...
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.
Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t...
Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable BEDs), bedtools genomecov/coverage (bedGraph tracks, per-target stats), samtools depth/coverage (per-base depth, per-con...
Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and...
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