GitHub
atacseq-qc
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...
Skills IA documentation scientific computing
Découvrez les skills documentation scientific computing, comparez leurs dépôts et consultez leurs instructions.
Catégories: documentation scientific computing
documentation scientific computing Effacer les filtres
Explorer
GitHub
known-motif-enrichment
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...
GitHub
chipseq-qc
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...
GitHub
replicates-incorporation
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...
GitHub
hic-loop-calling
This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.
GitHub
regulatory-community-analysis-chia-pet
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...
GitHub
global-methylation-profile
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...
GitHub
differential-methylation
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...
GitHub
hic-compartment-shift
This skill performs A/B compartment shift analysis between two Hi-C samples.
GitHub
track-generation
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...
GitHub
gsdworkflowresearch
Workflow for conducting research
GitHub
analyzing-research-documents
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.
GitHub
python-scientific-computing
Python for engineering analysis, numerical computing, and scientific workflows using NumPy, SciPy, SymPy
GitHub
numpy-numerical-analysis
NumPy for matrix operations, FFT, linear algebra, and numerical computations in marine engineering
GitHub
trend-modeling
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...
GitHub
trend-analysis
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...
GitHub
time-crystal-scheduling
Time crystal-inspired schedule stability analysis. Use when analyzing schedule churn, detecting natural periodicities, or optimizing for minimal disruption.
GitHub
research
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...
GitHub
comprehensive-research
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...
GitHub
scverse-compact
Compact single-cell analysis patterns with AnnData and Scanpy. Essential patterns for QC, preprocessing, clustering, and visualization.
GitHub
scverse
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...
GitHub
falcon-deep-research
Execute deep research protocols using the Falcon specialized research framework.
GitHub
deep-research
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...
GitHub
designing-experiments
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...
Le classement utilise les étoiles du dépôt GitHub indexé. Plusieurs skills peuvent partager ce nombre : ce n’est ni un nombre d’installations ni une note de qualité.