{"id":"https://openalex.org/W3178245612","doi":"https://doi.org/10.1093/bioinformatics/btab507","title":"CUT&amp;RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&amp;RUN and CUT&amp;Tag data analysis","display_name":"CUT&amp;RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&amp;RUN and CUT&amp;Tag data analysis","publication_year":2021,"publication_date":"2021-07-07","ids":{"openalex":"https://openalex.org/W3178245612","doi":"https://doi.org/10.1093/bioinformatics/btab507","mag":"3178245612","pmid":"https://pubmed.ncbi.nlm.nih.gov/34244724"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab507","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab507","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","license_id":"https://openalex.org/licenses/cc-by","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/btab507","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059967860","display_name":"Fulong Yu","orcid":"https://orcid.org/0000-0002-6100-8300"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fulong Yu","raw_affiliation_strings":["Department of Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA 02215, USA","Department of Pediatrics, Harvard Medical School , Boston, MA 02115, USA","Division of Hematology/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA","Program in Medical & Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Division of Hematology/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I1288882113"]},{"raw_affiliation_string":"Program in Medical & Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02115, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003021419","display_name":"Vijay G. Sankaran","orcid":"https://orcid.org/0000-0003-0044-443X"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijay G Sankaran","raw_affiliation_strings":["Department of Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA 02215, USA","Department of Pediatrics, Harvard Medical School , Boston, MA 02115, USA","Division of Hematology/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA","Program in Medical & Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Division of Hematology/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I1288882113"]},{"raw_affiliation_string":"Program in Medical & Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02115, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038587862","display_name":"Guo\u2010Cheng Yuan","orcid":"https://orcid.org/0000-0002-2283-4714"},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guo-Cheng Yuan","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","Department of Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA 02215, USA","Department of Pediatrics, Harvard Medical School , Boston, MA 02115, USA","Division of Hematology/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Pediatrics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Division of Hematology/Oncology, Boston Children\u2019s Hospital , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I1288882113"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5059967860"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I1288882113","https://openalex.org/I136199984","https://openalex.org/I4210117453"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.408,"has_fulltext":false,"cited_by_count":62,"citation_normalized_percentile":{"value":0.9385652,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"1","first_page":"252","last_page":"254"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10604","display_name":"RNA Research and Splicing","score":0.9975000023841858,"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/T11482","display_name":"RNA modifications and cancer","score":0.9965000152587891,"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/pipeline","display_name":"Pipeline (software)","score":0.739946722984314},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49249252676963806},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3575528562068939},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19267582893371582}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.739946722984314},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49249252676963806},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3575528562068939},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19267582893371582}],"mesh":[{"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab507","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab507","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34244724","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34244724","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:8696090","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8696090","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab507","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab507","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","license_id":"https://openalex.org/licenses/cc-by","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":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G605834453","display_name":null,"funder_award_id":"R01HG009663","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W2009259946","https://openalex.org/W2035330688","https://openalex.org/W2065549717","https://openalex.org/W2091626902","https://openalex.org/W2171808845","https://openalex.org/W2562443513","https://openalex.org/W2612550256","https://openalex.org/W2750049634","https://openalex.org/W2757704052","https://openalex.org/W2887694579","https://openalex.org/W2892648189","https://openalex.org/W2920191405","https://openalex.org/W2926894237","https://openalex.org/W2934716754","https://openalex.org/W2949529569","https://openalex.org/W2953322088","https://openalex.org/W2969437743","https://openalex.org/W2972263821","https://openalex.org/W2973032518","https://openalex.org/W2979464975","https://openalex.org/W2989061519","https://openalex.org/W3039566339","https://openalex.org/W3131634425","https://openalex.org/W3133082627","https://openalex.org/W6730523030"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"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":4},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2021-07-19T00:00:00"}
