Data Science & ML Agent Skills

Enzyme.jl Automatic Differentiation

Provides high-performance LLVM-level automatic differentiation for Julia code on CPU and GPU architectures.

Cognitive Surrogate Engine

Constructs high-fidelity psychological models from interaction patterns to predict intellectual trajectories and maintain authentic voice consistency.

Structured Decompositions

Applies category theory and sheaves on tree decompositions to solve complex combinatorial problems with Fixed-Parameter Tractable (FPT) algorithms.

Treasure Data Python SDK

Streamlines data querying and ingestion between Python analytical workflows and Treasure Data using the official pytd SDK.

Tool Experimenter

Systematically refines and validates research tools through multi-phase iterative testing and rigorous data-driven evaluation.

BibFilter

Filters and organizes bibliography entries by author, year, keyword, and entry type to streamline research workflows.

Hi-C A/B Compartment Analysis

Performs PCA-based A/B compartment calling and interaction analysis on Hi-C genomic datasets.

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.

RDKit Cheminformatics Toolkit

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

Local Methylation Profiling

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

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.

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.

Data Cleaning Pipeline Generator

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