{"doi":"10.1101/gr.262675.120","title":"MAnorm2 for quantitatively comparing groups of ChIP-seq samples","abstract":"Eukaryotic gene transcription is regulated by a large cohort of chromatin-associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2, a new computational tool for quantitatively comparing groups of ChIP-seq samples. MAnorm2 uses a hierarchical strategy for normalization of ChIP-seq data and assesses within-group variability of ChIP-seq signals based on an empirical Bayes framework. In this framework, MAnorm2 allows for abundant differential ChIP-seq signals between groups of samples as well as very different global within-group variability between groups. Using a number of real ChIP-seq data sets, we observed that MAnorm2 clearly outperformed existing tools for differential ChIP-seq analysis, especially when the groups of samples being compared had distinct global within-group variability.","journal":"Genome Research","year":2020,"id":118460,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":76,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9517,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":550702,"name":"Mushan Li","orcid":"0000-0003-2727-950X","position":1,"is_corresponding":false},{"id":550703,"name":"Haojie Chen","orcid":"0000-0002-4142-9829","position":2,"is_corresponding":false},{"id":551440,"name":"Fengxiang Tan","orcid":null,"position":3,"is_corresponding":false},{"id":56479,"name":"Jian Xu","orcid":"0000-0003-1988-7337","position":4,"is_corresponding":false},{"id":192317,"name":"David J Waxman","orcid":"0000-0001-7982-9206","position":5,"is_corresponding":false},{"id":550704,"name":"Yijing Zhang","orcid":"0000-0001-9568-9389","position":6,"is_corresponding":false},{"id":56477,"name":"Zhen Shao","orcid":"0000-0002-4934-4360","position":7,"is_corresponding":false},{"id":550701,"name":"Shiqi Tu","orcid":"0000-0003-3534-5714","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-18T23:13:58.531532Z","pmid":"33208455","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}