{"doi":"10.1101/2020.11.06.367409","title":"CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis","abstract":"Abstract ChIP-seq and ATAC-seq have become essential technologies used as effective methods of measuring protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates correct normalization between samples, adjustment of copy number variations, and integration of new downstream analysis tools. Here we present CoBRA, a modularized computational workflow which quantifies ChIP and ATAC-seq peak regions and performs unsupervised and supervised analysis. CoBRA provides a comprehensive state-of-the-art ChIP and ATAC-seq analysis pipeline that is usable by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference DB and pathway analysis. Code availability: https://bitbucket.org/cfce/cobra","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":123135,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9539,"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":565772,"name":"Avery Feit","orcid":"0000-0002-6586-9052","position":1,"is_corresponding":false},{"id":96016,"name":"Ariel Feiglin","orcid":"0000-0003-2862-7668","position":2,"is_corresponding":false},{"id":227594,"name":"Yingtian Xie","orcid":"0000-0003-0206-457X","position":3,"is_corresponding":false},{"id":246631,"name":"Nikolas Kesten","orcid":"0000-0002-9183-8778","position":4,"is_corresponding":false},{"id":418262,"name":"Len Taing","orcid":"0000-0001-7453-5372","position":5,"is_corresponding":false},{"id":565773,"name":"Joseph Perkins","orcid":"0000-0001-9436-7660","position":6,"is_corresponding":false},{"id":565774,"name":"Ningxuan Zhou","orcid":"0000-0002-7623-2276","position":7,"is_corresponding":false},{"id":243340,"name":"Shengqing Gu","orcid":"0000-0002-4200-0864","position":8,"is_corresponding":false},{"id":565775,"name":"Yihao Li","orcid":"0000-0003-1900-8099","position":9,"is_corresponding":false},{"id":565776,"name":"Paloma Cejas","orcid":"0000-0002-8417-4811","position":10,"is_corresponding":false},{"id":565777,"name":"Rinath Jeselsohn","orcid":"0000-0001-7996-7529","position":11,"is_corresponding":false},{"id":443,"name":"Myles Brown","orcid":"0000-0002-8213-1658","position":12,"is_corresponding":false},{"id":565778,"name":"X. Shirley Liu","orcid":"0000-0001-8588-1182","position":13,"is_corresponding":false},{"id":227618,"name":"Henry W. Long","orcid":"0000-0001-6849-6629","position":14,"is_corresponding":false},{"id":554209,"name":"Xintao Qiu","orcid":"0000-0002-8560-7017","position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":null,"created_at":"2026-07-18T23:14:59.547352Z","pmid":null,"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":[]}