Discover blockchain scientific computing skills, compare source repositories and read the instructions for each workflow.
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions...
This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.
Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read gro...
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and re...
Perform peak calling for ChIP-seq or ATAC-seq data using MACS3, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools, cooltools-tools, and plot-hic-tools servers.
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use thi...
This skill should be used when users need to perform known motif enrichment analysis on ChIP-seq, ATAC-seq, or other genomic peak files using HOMER (Hypergeometric Optimization of Motif EnRichment). It identifi...
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks...
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, gener...
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
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) fr...
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 prof...
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 Me...
This skill performs A/B compartment shift analysis between two Hi-C samples.
This skill generates normalized BigWig (.bw) tracks (and/or fold-change tracks) from BAM files for ATAC-seq and ChIP-seq visualization. It handles normalization (RPM or fold-change) and Tn5 offset correction au...
Workflow for conducting research
Extracts high-value insights from research documents, RCAs, design docs, and memos - filters aggressively to return only actionable information. Research equivalent of analyzing-implementations skill.
Python for engineering analysis, numerical computing, and scientific workflows using NumPy, SciPy, SymPy
NumPy for matrix operations, FFT, linear algebra, and numerical computations in marine engineering
This skill should be used when the user asks to "model trends with limited data", "three-valued logic analysis", "scenario generation", "transitional graphs", "qualitative trend analysis", "uncertain data analy...
This skill should be used when the user asks to "identify trends", "analyze market trends", "trend forecasting", "macro trends", "micro trends", "emerging patterns", "future projections", "industry trends", or...
Time crystal-inspired schedule stability analysis. Use when analyzing schedule churn, detecting natural periodicities, or optimizing for minimal disruption.
Get AI-synthesized research on any topic with citations, directly in your terminal. Supports structured JSON output for pipelines. Use when you need comprehensive research grounded in web data without writing c...
The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.