Discover documentation scientific computing skills, compare source repositories and read the instructions for each workflow.
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...
Multi-phase research orchestration for thorough codebase, documentation, and external knowledge investigation. Invoked by /ai-eng/research command. Use when conducting deep analysis, exploring codebases, invest...
Compact single-cell analysis patterns with AnnData and Scanpy. Essential patterns for QC, preprocessing, clustering, and visualization.
Single-cell analysis patterns with AnnData and Scanpy. Use when working with single-cell RNA-seq data, creating or manipulating AnnData objects, performing quality control, normalization, dimensionality reducti...
Execute deep research protocols using the Falcon specialized research framework.
Conduct comprehensive, multi-source research on any topic using web search, documentation lookup, and critical analysis. This skill should be used when users request thorough investigation, deep research, or co...
Interactive guidance for building Sun lab VR experiment configurations using MCP tools and CLI commands. Covers template discovery, experiment configuration generation, and Unity template creation. Use when cre...
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.