batch-analysislisted

# Batch Analysis of ENCODE Experiments ## When to Use - User wants to process, compare, or QC multiple ENCODE experiments simultaneously - User asks about "batch analysis", "bulk processing", "experiment comparison table", or "multi-sample QC" - User needs to screen 5+ experiments for quality before analysis - User wants a summary report or comparison table across many experiments - Example queries: "QC all H3K27ac experiments in liver", "compare quality across 10 ChIP-seq datasets", "batch download and summarize my experiment collection" Help the user perform systematic batch operations across multiple ENCODE experiments. When working with 5 or more experiments -- common in cross-tissue comparisons, multi-mark epigenomic profiling, or large-scale data collection -- individual experiment-by-experiment workflows become impractical and error-prone. This skill covers batch discovery, quality screening, download management, pairwise comparison, and report generation using the ENCODE MCP tools. ## Literature Foundation | Reference | Journal | Key Contribution | DOI | Citations | |-----------|---------|-----------------|-----|-----------| | ENCODE Project Consortium (2020) | Nature | Expanded encyclopedia of 926,535 candidate cis-regulatory elements across 1,698 cell types; framework for large-scale integrative analysis | [10.1038/s41586-020-2493-4](https://doi.org/10.1038/s41586-020-2493-4) | ~2,000 | | Hitz et al. (2023) | Nucleic Acids Research | The ENCODE Uniform Processi