Tag: atac-seq
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…
ENCODE Multi-Omics Data Integration
Integrates multiple ENCODE data types, including RNA-seq, ATAC-seq, and ChIP-seq, to construct a comprehensive regulatory landscape for specific tissues or cell types. It enables chromatin state annotation, enhancer-gene linkage, and the ch…
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.
Setup reproducible bioinformatics environments for ENCODE
This skill provisions fully reproducible, version-pinned computational environments for diverse ENCODE assays, generating conda definitions, R/Bioconductor scripts, and Python requirements. It simplifies the setup of complex pipelines (e.g.…
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…