Data Science & ML Agent Skills

Nested TAD Detection

Identifies hierarchical Topologically Associating Domain (TAD) structures from Hi-C contact maps using the OnTAD algorithm.

Methylation & Chromatin Feature Correlation

Integrates DNA methylation data with chromatin features like ATAC-seq and histone marks to analyze epigenomic relationships and regulatory patterns.

Chromatin State Inference

Analyzes histone modification ChIP-seq data to segment the genome into discrete chromatin states using ChromHMM workflows.

BAM Filtration

Filters raw BAM files by removing mitochondrial reads, PCR duplicates, and blacklisted regions to prepare genomic data for peak calling.

De Novo Motif Discovery

Identifies novel and known transcription factor binding motifs within genomic regions or gene promoters using the HOMER analysis suite.

Hi-C Matrix Quality Control

Performs standardized quality control analysis on Hi-C contact matrices to evaluate genomic data depth, uniformity, and reproducibility.

Hi-C Compartment Shift Analysis

Performs A/B compartment shift analysis between Hi-C samples using PC1 eigenvector values and replicate-aware statistical methods.

Global Methylation Profiling

Performs genome-wide DNA methylation analysis to characterize patterns, genomic feature distributions, and sample similarities from sequencing data.

Differential TAD Analysis

Performs differential topologically associating domain (TAD) analysis to identify significant chromatin architecture changes between experimental conditions using HiCExplorer.

Local Methylation Profiling

Generates and visualizes DNA methylation distribution patterns around specific genomic features such as promoters, enhancers, or transcription factor binding sites.

Memvid Local RAG

Enables local semantic search and document indexing for PDF, DOCX, and XLSX files directly within Claude Code.

Hi-C TAD Calling & Visualization

Identifies topologically associating domains (TADs) from Hi-C data and generates high-resolution contact map visualizations with boundary overlays.

Alignment Quality Control

Evaluates technical mapping statistics for ChIP-seq and ATAC-seq BAM files to ensure data integrity and aligner performance before downstream analysis.

Genomic Feature Annotation & Visualization

Annotates genomic regions with biological features and generates visual distribution summaries using the Homer bioinformatics suite.

Replicates Incorporation

Manages genomic experimental reproducibility by pooling BAM files, generating pseudo-replicates, and performing IDR or consensus peak analysis.

Loop Annotation

Annotates chromatin loops with regulatory and structural information, including enhancer-promoter mappings and CTCF-peak overlap.

Differential Methylation Analysis

Identifies differential DNA methylation regions and cytosines between experimental conditions using WGBS methylation tracks.

Known Motif Scanning

Identifies and maps transcription factor binding motifs within genomic regions like ChIP-seq and ATAC-seq peaks using HOMER.

Methylation Variability Analysis

Quantifies CpG-level methylation variability and epigenetic heterogeneity from whole-genome bisulfite sequencing data using standardized statistical workflows.

Integrative Methylation-Expression Analysis

Integrates differential methylation and gene expression datasets to identify coordinated epigenetic regulation patterns and classify regulatory relationships.

Nushell Data Processing

Enables high-performance data manipulation and analysis in Nushell using Polars DataFrames and LazyFrames.

RDKit Cheminformatics Toolkit

Performs advanced molecular analysis, descriptor calculation, and chemical informatics using the RDKit library.

Vector Field Dynamics

Models and analyzes dynamical systems by assigning vectors to points in phase space to define complex flows and trajectories.

Research Ethics & Compliance

Provides PhD-level guidance on research ethics, IRB compliance, and data privacy analysis for study protocols and algorithmic models.

Times Square Integration

Integrates the Times Square notebook execution system into web applications using established patterns for data fetching, real-time updates, and URL management.

Data Cleaning Pipeline Generator

Automates the creation of robust data cleaning and preprocessing pipelines for Python-based data science workflows.

PolicyEngine Aggregation Patterns

Standardizes variable summation and entity aggregation within the PolicyEngine microsimulation framework.

DisCoPy String Diagram Framework

Computes and visualizes monoidal categories, quantum circuits, and natural language structures using string diagrams.

Gemini Prompt Engineering

Optimizes AI workflows by providing expert guidance and implementation patterns for Google Gemini models.

Multiversal Finance

Implements decentralized prediction markets for pattern discovery based on curiosity-driven compression progress metrics.