{"id":"https://openalex.org/W2792006949","doi":"https://doi.org/10.1093/bioinformatics/bty141","title":"esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis","display_name":"esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis","publication_year":2018,"publication_date":"2018-03-06","ids":{"openalex":"https://openalex.org/W2792006949","doi":"https://doi.org/10.1093/bioinformatics/bty141","mag":"2792006949","pmid":"https://pubmed.ncbi.nlm.nih.gov/29522192"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty141","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty141","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/bty141","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100625375","display_name":"Wei Zheng","orcid":"https://orcid.org/0000-0003-2060-7486"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zheng Wei","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100761365","display_name":"Wei Zhang","orcid":"https://orcid.org/0000-0003-4264-5758"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Zhang","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103825411","display_name":"Huan Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huan Fang","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033512723","display_name":"Yanda Li","orcid":"https://orcid.org/0000-0002-9439-202X"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanda Li","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008093795","display_name":"Xiaowo Wang","orcid":"https://orcid.org/0000-0003-2965-8036"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaowo Wang","raw_affiliation_strings":["Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5008093795"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6892,"has_fulltext":false,"cited_by_count":59,"citation_normalized_percentile":{"value":0.90961839,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"34","issue":"15","first_page":"2664","last_page":"2665"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.9854798316955566},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.745373010635376},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6507783532142639},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6487715244293213},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.6476863622665405},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6185207962989807},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5712616443634033},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5185171365737915},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.513151228427887},{"id":"https://openalex.org/keywords/source-lines-of-code","display_name":"Source lines of code","score":0.47201961278915405},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.4399200677871704},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3943276107311249},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38287532329559326},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3337146043777466},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.30617403984069824},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2463376224040985},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12054756283760071},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10771110653877258}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9854798316955566},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.745373010635376},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6507783532142639},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6487715244293213},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.6476863622665405},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6185207962989807},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5712616443634033},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5185171365737915},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.513151228427887},{"id":"https://openalex.org/C199519371","wikidata":"https://www.wikidata.org/wiki/Q942695","display_name":"Source lines of code","level":3,"score":0.47201961278915405},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.4399200677871704},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3943276107311249},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38287532329559326},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3337146043777466},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.30617403984069824},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2463376224040985},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12054756283760071},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10771110653877258},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty141","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty141","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29522192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29522192","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5027382","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6061683","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty141","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty141","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5799999833106995}],"awards":[{"id":"https://openalex.org/G5808002254","display_name":null,"funder_award_id":"61773230","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5814160623","display_name":null,"funder_award_id":"61721003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7929829911","display_name":null,"funder_award_id":"31371341","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324856","display_name":"Southeast University","ror":"https://ror.org/04ct4d772"},{"id":"https://openalex.org/F4320335923","display_name":"Open Research Fund of State Key Laboratory of Bioelectronics","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1900337607","https://openalex.org/W2117757143","https://openalex.org/W2118515267","https://openalex.org/W2143215863","https://openalex.org/W2170551349","https://openalex.org/W2263582186","https://openalex.org/W2952358992"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W2128360321","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2792006949","https://openalex.org/W2098339479"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}