Tag: chip-seq
Comprehensive ENCODE Data Quality Assessment Skill
This skill evaluates the reliability of ENCODE experiments by interpreting multiple orthogonal quality metrics, such as FRiP, NSC, and NRF, alongside official audit flags. It provides deep guidance for filtering and comparing data across va…
ENCODE ChIP-seq Analysis Pipeline for Peak Calling
This skill executes a complete, standards-compliant ChIP-seq workflow, processing raw FASTQ files through alignment, MACS2 peak calling, and IDR analysis. It generates comprehensive peak sets and signal tracks, adhering to ENCODE guidelines…
ENCODE Peak Annotation and Functional Enrichment
Annotate ENCODE genomic peaks with regulatory features and nearby genes using ChIPseeker and GREAT. The workflow enables genomic feature distribution analysis and functional enrichment via clusterProfiler.
Aggregate histone mark peaks across multiple studies
This skill constructs comprehensive histone mark maps by aggregating narrowPeak data from multiple ENCODE experiments, donors, and labs into a single union peak set. It handles complex data quality steps, including ENCODE blocklist filterin…
Visualize ENCODE genomic data for publication
This skill facilitates the creation of publication-quality visualizations of ENCODE genomic data, covering deepTools heatmaps, signal profiles, and interactive IGV browser views. It guides users through advanced techniques like computeMatri…
Assess ENCODE experiment quality metrics and flags
This skill guides the rigorous assessment of ENCODE data quality by interpreting standard metrics (e.g., FRiP, NSC, IDR) and analysing audit flags. It provides context on determining data reliability across various assays and biological sys…
ENCODE ChIP-seq Processing Pipeline
This Nextflow-based pipeline executes the complete ENCODE ChIP-seq processing workflow, transforming raw FASTQ files into peaks and signal tracks. It handles quality control, alignment, peak calling with MACS2, and IDR analysis using Docker…
Integrating JASPAR Motifs with ENCODE ChIP-seq
Integrate JASPAR transcription factor binding profiles with ENCODE ChIP-seq peaks to validate binding targets and discover co-factors. This skill enables scanning regulatory regions for motif enrichment and assessing the impact of genomic v…
Aggregate Histone ChIP-seq Peaks Across Studies
This skill aggregates histone ChIP-seq peaks from multiple ENCODE experiments into a unified, confidence-annotated map. It manages cross-lab batch effects and applies rigorous filtering, including ENCODE blocklist removal and signal value q…