Tag: chromatin-accessibility
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…
ENCODE ATAC-seq Pipeline for Chromatin Accessibility Analysis
This skill executes the comprehensive ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and filtering. It generates high-quality peak calls and signal tracks suitable for detailed chromatin acces…
Aggregate comprehensive open chromatin accessibility maps
This skill builds a comprehensive union map of open chromatin regions by aggregating and merging ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments. It handles cross-platform variation, applies necessary filtering (su…
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…
ENCODE ATAC-seq Pipeline for Chromatin Accessibility
This tool executes the full ENCODE ATAC-seq workflow, processing raw FASTQ files through alignment, Tn5 offset correction, and rigorous filtering. It generates nucleosome-free peaks and signal tracks following established ENCODE standards.
Integrate multi-omics for regulatory landscape
This skill integrates diverse ENCODE datasets, including RNA-seq, ATAC-seq, and various ChIP-seq assays, to construct a comprehensive regulatory landscape. It allows users to map cell-type-specific regulatory elements by correlating gene ex…
Comparing ENCODE Experiments Across Biosamples
This skill enables the systematic comparison of ENCODE experiments across various tissues, cell lines, and biosamples to identify tissue-specific regulatory patterns. It facilitates the identification of constitutive versus variable regulat…
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…