{"doi":"10.1093/bioinformatics/btab438","title":"Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data","abstract":"SUMMARY: Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Here, we present methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin accessibility landscapes. Methylscaper implements a weighted principal component analysis that orders DNA molecules, each providing a record of the chromatin state of one epiallele, and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation. We demonstrate methylscaper's utility on a long-read, single-molecule methyltransferase accessibility protocol for individual templates (MAPit-BGS) dataset and a single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) dataset. In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets. AVAILABILITY AND IMPLEMENTATION: Methylscaper, is implemented in R (version > 4.1) and available on Bioconductor: https://bioconductor.org/packages/methylscaper/, GitHub: https://github.com/rhondabacher/methylscaper/, and Web: https://methylscaper.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2021,"id":192967,"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":11,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9254,"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":258271,"name":"Marie‐Pierre L. Gauthier","orcid":"0009-0002-1936-2231","position":1,"is_corresponding":false},{"id":760732,"name":"Carolina Pardo‐Díaz","orcid":"0000-0002-7259-1183","position":2,"is_corresponding":false},{"id":761385,"name":"Russell P. Darst","orcid":null,"position":3,"is_corresponding":false},{"id":515426,"name":"Kevin Kapadia","orcid":null,"position":4,"is_corresponding":false},{"id":515425,"name":"Hadley Browder","orcid":null,"position":5,"is_corresponding":false},{"id":761386,"name":"Eliza Morton","orcid":null,"position":6,"is_corresponding":false},{"id":77359,"name":"Alberto Riva","orcid":"0000-0001-9150-8333","position":7,"is_corresponding":false},{"id":447551,"name":"Michael P. Kladde","orcid":"0000-0001-7951-9291","position":8,"is_corresponding":false},{"id":86476,"name":"Rhonda Bacher","orcid":"0000-0001-5787-476X","position":9,"is_corresponding":false},{"id":362463,"name":"Parker Knight","orcid":"0000-0002-1141-3201","position":0,"is_corresponding":true}],"reference_count":22,"raw_metadata":null,"created_at":"2026-07-18T23:49:47.463744Z","pmid":"34125875","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":[]}