This skill performs differential DNA methylation analysis (DMRs and DMCs) between experimental conditions using WGBS methylation tracks (BED/BedGraph). It standardizes input files into per-sample four-column Metilene tables, constructs a merged methylation matrix, runs Metilene for DMR detection, filters the results, and generates quick visualizations.
This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It compares Hi-C contact matrices between two conditions based on existing TAD definitions to identify significantly altered chromatin domains.
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CTCF peak or other target regions).
This skill manages experimental reproducibility, pooling, and consensus strategies. This skill operates in two distinct modes based on the input state. (1) Pre-Peak Calling (BAM Mode): It merges all BAMs, generate the merge BAM file to prepare for track generation and (if provided with >3 biological replicates) splits them into 2 balanced "pseudo-replicates" to prepare for peak calling. (2) Post-Peak Calling (Peak Mode): If provided with peak files (only support two replicates, derived from either 2 true replicates or 2 pseudo-replicates), it performs IDR (Irreproducible Discovery Rate) analysis, filters non-reproducible peaks, and generates a final "conservative" or "optimal" consensus peak set. Trigger this skill when you need to handle more than two replicates (creating pseudo-reps) OR when you need to merge peak lists.
This skill provides a complete and streamlined workflow for performing methylation variability and epigenetic heterogeneity analysis from whole-genome bisulfite sequencing (WGBS) data. It is designed for researchers who want to quantify CpG-level variability across biological samples or conditions, identify highly variable CpGs (HVCs), and explore epigenetic heterogeneity.
This skill performs protein-mediated regulatory community analysis from ChIA-PET datasets and provide a way for visualizing the communities. Use this skill when you have a annotated peak file (in BED format) from ChIA-PET experiment and you want to identify the protein-mediated regulatory community according to the BED and BEDPE file from ChIA-PET.
This skill performs genome-wide DNA methylation profiling. It supports single-sample and multi-sample workflows to compute methylation density distributions, genomic feature distribution of the methylation profile, and sample-level clustering/PCA. Use it when you want to systematically characterize global methylation patterns from WGBS or similar per-CpG methylation call files.
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with coordinated epigenetic regulation. It provides preprocessing and integration workflows, using promoter-level methylation–expression relationships.
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bisulfite sequencing (WGBS) methylation calls. The pipeline provides high-resolution enhancer-like LMRs, promoter-associated UMRs, and large-scale PMDs characteristic of reprogramming, aging, or cancer methylomes, enabling integration with chromatin accessibility, TF binding, and genome architecture analyses.
This skill identifies novel transcription factor binding motifs in the promoter regions of genes, or directly from genomic regions of interest such as ChIP-seq peaks, ATAC-seq accessible sites, or differentially acessible regions. It employs HOMER (Hypergeometric Optimization of Motif Enrichment) to detect both known and previously uncharacterized sequence motifs enriched within the supplied genomic intervals. Use the skill when you need to uncover sequence motifs enriched or want to know which TFs might regulate the target regions.
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined by position-specific scoring matrices (PSSMs) from known motif databases. Use this skill when you need to detect the presence and precise genomic coordinates of known TF binding motifs within experimentally defined regions such as ChIP-seq or ATAC-seq peaks.
Anthropic-aligned medical safety evaluation with pass^k metrics, failure taxonomy, and anti-gaming graders
Validate WCAG compliance and accessibility standards (ARIA, keyboard navigation). Use when auditing WCAG compliance or screen reader compatibility. Trigger with phrases like "scan accessibility", "check WCAG compliance", or "validate screen readers".
Systematic approach to discovering novel vulnerabilities through code analysis, fuzzing, and attack surface research
Use and troubleshoot the Memory MCP server for episodic memory retrieval and pattern analysis. Use this skill when working with MCP server tools (query_memory, analyze_patterns, advanced_pattern_analysis), validating the MCP implementation, or debugging MCP server issues.
Systematic methodology for developing reliable exploits from vulnerability discovery to weaponization
Generate PRISMA 2020 flow diagrams for systematic reviews. Use when: (1) Conducting systematic literature reviews, (2) Documenting screening process, (3) Reporting study selection for publications, (4) Demonstrating PRISMA compliance, (5) Creating transparent review methodology documentation.
Design rigorous experiments following best practices. Use when: (1) Planning research studies, (2) Grant proposal development, (3) Pre-registration, (4) Ensuring internal validity, (5) Meeting NIH rigor standards.
Develop IRB/ethics protocols for human subjects research. Use when: (1) Planning studies involving humans, (2) Preparing IRB applications, (3) Ensuring ethical compliance, (4) Addressing informed consent.
Implement proper randomization procedures for experiments. Use when: (1) Assigning participants to conditions, (2) Ensuring unbiased allocation, (3) Meeting CONSORT standards, (4) Pre-registration.
Cosmos SDK module development patterns and conventions for Celestia
