Tag: dnase-seq

Type: All Skills Tools
Tags: mcp automation llm cli code-review unity typescript genomics game-development bioinformatics debugging documentation cloudbase ai-agents agentic-workflow devops llm-agent workflow-automation encode code-analysis
skill ★ 34

ENCODE DNase-seq Pipeline for Hotspots and Footprints

This skill executes the comprehensive ENCODE DNase-seq pipeline, processing paired FASTQ reads to identify DNase hypersensitive sites (DHSs) and perform TF footprinting analysis. It utilizes Nextflow to generate critical data products, incl…

ammawla/encode-toolkit dnase-seq hotspots footprinting chromatin-accessibility
skill ★ 34

DNase-seq pipeline for accessibility and footprints

Executes a comprehensive DNase-seq workflow, processing paired-end FASTQ reads to identify DNase hypersensitive sites (DHSs) and perform transcription factor footprinting. The pipeline leverages Nextflow to manage alignment, peak calling vi…

ammawla/encode-toolkit dnase-seq chromatin-accessibility hotspot-calling footprinting
skill ★ 34

Aggregate Chromatin Accessibility Peaks Across Studies

This skill generates a comprehensive union map of open chromatin by merging ATAC-seq and DNase-seq narrowPeak data from multiple ENCODE experiments. It handles cross-platform variation and applies rigorous filtering and confidence annotatio…

ammawla/encode-toolkit chromatin-accessibility atac-seq dnase-seq peak-aggregation