AIPOCH

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.

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Use when refactoring research code for publication, adding documentation to existing analysis scripts, creating reproducible computational workflows, or preparing code for sharing with collaborators. Transforms research code into publication-ready, reproducible workflows. Adds documentation, implements error handling, creates environment specifications, and ensures computational reproducibility for scientific publications.

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Screen full-text papers against inclusion/exclusion criteria, with optional PubMed metadata check using PMID. Use when the user needs to evaluate a paper for a meta-analysis.

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Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generate...

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Use facs gating viz style for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

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Machine learning toolkit for genomic interval (BED) data; use it when you need to tokenize BED collections and train embeddings for regions/cells/labels, build consensus peak universes, or run similarity search and downstream ML on chromatin accessibility datasets.

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Generates PI(E)COS structure (Population, Intervention, Comparator, Outcomes, Study Design) from Meta-analysis or study titles. Use when the user wants to extract these elements from a title.

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Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots. Supports CNV calling, segmentation, and visualization for cancer genomics and rare disease analysis.

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Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.

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Parse Flow Cytometry Standard (FCS) files v2.0–3.1 and extract events/metadata for preprocessing workflows (e.g., when you need NumPy arrays, channel info, or CSV/DataFrame export from cytometry files).

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This skill is applicable when using LaminDB. LaminDB is an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR-compliant. It is suitable for managing biological datasets (scRNA-seq, spatial transcriptomics, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakes, or ensuring data lineage and reproducibility in biological research. It covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integration with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

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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.

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Draw ROB2 risk-of-bias plots, including a Traffic Light Plot and a Summary Bar Plot. Input is a CSV file with ROB2 assessments for each study; output are two PNG plot files.

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Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

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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.

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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.

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Digital pathology image processing toolkit for whole slide images (WSI). Supports WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

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A high-performance Rust toolkit (with Python bindings and a CLI) for genomic interval analysis; use it when you need fast overlap queries, coverage track generation, genomic tokenization for ML, reference sequence verification, or fragment processing.

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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.

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Screens research papers based on title/abstract and inclusion criteria, providing a structured Yes/No/Maybe decision. Use when you need to filter literature for meta-analysis or systematic reviews.

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Performs epidemiological analyses including disease modeling (SIR/SEIR), outbreak investigation, risk factor identification, incidence/prevalence estimation, and causal inference from observational data; trigger when users discuss disease spread, public health data, or populat...

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Use when cleaning clinical trial data, preparing data for FDA/EMA submission, standardizing SDTM datasets, handling missing values in clinical studies, detecting outliers in lab results, or converting raw CRF data to CDISC format. Cleans and standardizes clinical trial data fo...

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Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.

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Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.

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