{"doi":"10.1186/s12859-021-04097-5","title":"A flexible ChIP-sequencing simulation toolkit","abstract":"BACKGROUND: A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this challenge, but existing frameworks are either too cumbersome to apply genome-wide or unable to model a number of important experimental conditions in ChIP-seq. RESULTS: We present ChIPs, a toolkit for rapidly simulating ChIP-seq data using statistical models of key experimental steps. We demonstrate how ChIPs can be used for a range of applications, including benchmarking analysis tools and evaluating the impact of various experimental parameters. ChIPs is implemented as a standalone command-line program written in C++ and is available from https://github.com/gymreklab/chips . CONCLUSIONS: ChIPs is an efficient ChIP-seq simulation framework that generates realistic datasets over a flexible range of experimental conditions. It can serve as an important component in various ChIP-seq analyses where ground truth data are needed.","journal":"BMC Bioinformatics","year":2021,"id":199973,"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":8,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.943,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":566348,"name":"Michael Lamkin","orcid":"0000-0001-5797-1914","position":1,"is_corresponding":false},{"id":539641,"name":"Yutong Qiu","orcid":"0000-0001-6058-1212","position":2,"is_corresponding":false},{"id":777053,"name":"Kevin Ren","orcid":"0000-0002-3841-591X","position":3,"is_corresponding":false},{"id":855,"name":"Alon Goren","orcid":"0000-0001-5669-9357","position":4,"is_corresponding":false},{"id":314350,"name":"Melissa Gymrek","orcid":"0000-0002-6086-3903","position":5,"is_corresponding":false},{"id":560699,"name":"An Zheng","orcid":"0000-0002-3689-2712","position":0,"is_corresponding":true}],"reference_count":20,"raw_metadata":null,"created_at":"2026-07-18T23:50:44.479665Z","pmid":"33879052","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":[]}