{"id":"https://openalex.org/W3203401351","doi":"https://doi.org/10.1093/bioinformatics/btab680","title":"ShinyArchR.UiO: user-friendly,integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR","display_name":"ShinyArchR.UiO: user-friendly,integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR","publication_year":2021,"publication_date":"2021-09-24","ids":{"openalex":"https://openalex.org/W3203401351","doi":"https://doi.org/10.1093/bioinformatics/btab680","mag":"3203401351","pmid":"https://pubmed.ncbi.nlm.nih.gov/34586377"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab680","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab680","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/3/834/49008050/btab680.pdf","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://academic.oup.com/bioinformatics/article-pdf/38/3/834/49008050/btab680.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085108207","display_name":"Ankush Sharma","orcid":"https://orcid.org/0000-0002-1399-7503"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ankush Sharma","raw_affiliation_strings":["Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway","Department of Biosciences, University of Oslo , 0316 Oslo, Norway","Department of Informatics, Institute of Basic Medical Sciences, University of Oslo , 0316 Oslo, Norway","Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway","PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo , 0316 Oslo, Norway"],"affiliations":[{"raw_affiliation_string":"Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Biosciences, University of Oslo , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Informatics, Institute of Basic Medical Sciences, University of Oslo , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035810113","display_name":"Akshay Akshay","orcid":"https://orcid.org/0000-0003-3186-7478"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Akshay Akshay","raw_affiliation_strings":["Urology Research Laboratory, Department for BioMedical Research DBMR, University of Bern , 3012 Bern, Switzerland"],"affiliations":[{"raw_affiliation_string":"Urology Research Laboratory, Department for BioMedical Research DBMR, University of Bern , 3012 Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069454824","display_name":"Marie Rogne","orcid":"https://orcid.org/0000-0002-3594-9000"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Marie Rogne","raw_affiliation_strings":["Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway","Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway"],"affiliations":[{"raw_affiliation_string":"Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066558348","display_name":"Ragnhild Eskeland","orcid":"https://orcid.org/0000-0003-2789-3171"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ragnhild Eskeland","raw_affiliation_strings":["Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway","Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway","PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo , 0316 Oslo, Norway"],"affiliations":[{"raw_affiliation_string":"Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo , 0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5066558348","https://openalex.org/A5085108207"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4879,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62549739,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"38","issue":"3","first_page":"834","last_page":"836"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9751999974250793,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/visualization","display_name":"Visualization","score":0.7547266483306885},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.7346524596214294},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6745184063911438},{"id":"https://openalex.org/keywords/open-source-software","display_name":"Open source software","score":0.5842734575271606},{"id":"https://openalex.org/keywords/user-friendly","display_name":"User Friendly","score":0.4893574118614197},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4587685167789459},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30280691385269165},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12782517075538635}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7547266483306885},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.7346524596214294},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6745184063911438},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.5842734575271606},{"id":"https://openalex.org/C61437842","wikidata":"https://www.wikidata.org/wiki/Q281291","display_name":"User Friendly","level":2,"score":0.4893574118614197},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4587685167789459},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30280691385269165},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12782517075538635}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab680","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab680","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/3/834/49008050/btab680.pdf","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:34586377","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34586377","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:pubmedcentral.nih.gov:8756194","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8756194","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.duo.uio.no:10852/91066","is_oa":true,"landing_page_url":"http://hdl.handle.net/10852/91066","pdf_url":null,"source":{"id":"https://openalex.org/S4306401717","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab680","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab680","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/3/834/49008050/btab680.pdf","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":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G3748656914","display_name":null,"funder_award_id":"Norway","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G5358662222","display_name":null,"funder_award_id":"262652","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"}],"funders":[{"id":"https://openalex.org/F4320323260","display_name":"Universitetet i Oslo","ror":"https://ror.org/01xtthb56"},{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3203401351.pdf","grobid_xml":"https://content.openalex.org/works/W3203401351.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W1602702667","https://openalex.org/W2069089843","https://openalex.org/W2117757143","https://openalex.org/W2949177718","https://openalex.org/W3034491533","https://openalex.org/W3131634425"],"related_works":["https://openalex.org/W4376877853","https://openalex.org/W1493891899","https://openalex.org/W4250928611","https://openalex.org/W4232280318","https://openalex.org/W166480398","https://openalex.org/W167327709","https://openalex.org/W4387839566","https://openalex.org/W4210922265","https://openalex.org/W4319870556","https://openalex.org/W2084742289"],"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":2},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
