{"id":"https://openalex.org/W3003909932","doi":"https://doi.org/10.1093/bioinformatics/btaa073","title":"<i>Coolpup.py:</i> versatile pile-up analysis of Hi-C data","display_name":"<i>Coolpup.py:</i> versatile pile-up analysis of Hi-C data","publication_year":2020,"publication_date":"2020-01-27","ids":{"openalex":"https://openalex.org/W3003909932","doi":"https://doi.org/10.1093/bioinformatics/btaa073","mag":"3003909932","pmid":"https://pubmed.ncbi.nlm.nih.gov/32003791"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa073","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/10/2980/33204367/btaa073.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","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://academic.oup.com/bioinformatics/article-pdf/36/10/2980/33204367/btaa073.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021382553","display_name":"Ilya M. Flyamer","orcid":"https://orcid.org/0000-0002-4892-4208"},"institutions":[{"id":"https://openalex.org/I4210158898","display_name":"Institute of Genetics and Cancer","ror":"https://ror.org/05hygey35","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210158898","https://openalex.org/I90344618","https://openalex.org/I98677209"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Ilya M Flyamer","raw_affiliation_strings":["MRC Human Genetics Unit , Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK"],"affiliations":[{"raw_affiliation_string":"MRC Human Genetics Unit , Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK","institution_ids":["https://openalex.org/I4210158898","https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064862532","display_name":"Robert S. Illingworth","orcid":"https://orcid.org/0000-0001-9275-1933"},"institutions":[{"id":"https://openalex.org/I4210108209","display_name":"MRC Centre for Regenerative Medicine","ror":"https://ror.org/01x802g65","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210108209","https://openalex.org/I90344618","https://openalex.org/I98677209"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Robert S Illingworth","raw_affiliation_strings":["MRC Centre for Regenerative Medicine , Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK"],"affiliations":[{"raw_affiliation_string":"MRC Centre for Regenerative Medicine , Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK","institution_ids":["https://openalex.org/I4210108209","https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076700359","display_name":"Wendy A. Bickmore","orcid":"https://orcid.org/0000-0001-6660-7735"},"institutions":[{"id":"https://openalex.org/I4210158898","display_name":"Institute of Genetics and Cancer","ror":"https://ror.org/05hygey35","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4210158898","https://openalex.org/I90344618","https://openalex.org/I98677209"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Wendy A Bickmore","raw_affiliation_strings":["MRC Human Genetics Unit , Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK"],"affiliations":[{"raw_affiliation_string":"MRC Human Genetics Unit , Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK","institution_ids":["https://openalex.org/I4210158898","https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5021382553"],"corresponding_institution_ids":["https://openalex.org/I4210158898","https://openalex.org/I98677209"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":15.7675,"has_fulltext":true,"cited_by_count":229,"citation_normalized_percentile":{"value":0.99260918,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"36","issue":"10","first_page":"2980","last_page":"2985"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13650","display_name":"Computational Physics and Python Applications","score":0.9847000241279602,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13650","display_name":"Computational Physics and Python Applications","score":0.9847000241279602,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.944100022315979,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9350000023841858,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pile","display_name":"Pile","score":0.7681015133857727},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4968412220478058},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2976565361022949}],"concepts":[{"id":"https://openalex.org/C119560385","wikidata":"https://www.wikidata.org/wiki/Q7193850","display_name":"Pile","level":2,"score":0.7681015133857727},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4968412220478058},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2976565361022949}],"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":"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaa073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa073","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/10/2980/33204367/btaa073.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","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:32003791","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32003791","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:pure.ed.ac.uk:publications/7c2c516b-9d8a-47f3-a39f-15dbe20dbcf9","is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.11820/7c2c516b-9d8a-47f3-a39f-15dbe20dbcf9","pdf_url":"https://www.pure.ed.ac.uk/ws/files/134475161/btaa073.pdf","source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"","raw_type":""},{"id":"pmh:oai:pure.ed.ac.uk:publications/7c2c516b-9d8a-47f3-a39f-15dbe20dbcf9","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/7c2c516b-9d8a-47f3-a39f-15dbe20dbcf9","pdf_url":"https://www.research.ed.ac.uk/files/134475161/btaa073.pdf","source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Flyamer, I M, Illingworth, R & Bickmore, W 2020, 'Coolpup.py: versatile pile-up analysis of Hi-C data', Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa073","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:7214034","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7214034","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/btaa073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa073","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/10/2980/33204367/btaa073.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","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","score":0.4099999964237213,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1638921556","display_name":null,"funder_award_id":"MR/S007644/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G4585706523","display_name":null,"funder_award_id":"MC_ UU_00007/2","funder_id":"https://openalex.org/F4320315019","funder_display_name":"Simons Foundation Autism Research Initiative"},{"id":"https://openalex.org/G5379032847","display_name":null,"funder_award_id":"MR/K017047/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G5964716100","display_name":null,"funder_award_id":"MC_ UU_00007/2","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G6971111784","display_name":null,"funder_award_id":"MC_UU_00007/2","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7041107416","display_name":"Cell-Specific PRC1 Accessory Proteins and the Regulation of Mammalian Neurodevelopment","funder_award_id":"MR/S007644/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320315019","display_name":"Simons Foundation Autism Research Initiative","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320328997","display_name":"Simons Initiative for the Developing Brain","ror":null},{"id":"https://openalex.org/F4320331788","display_name":"Darwin Trust of Edinburgh","ror":null},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3003909932.pdf","grobid_xml":"https://content.openalex.org/works/W3003909932.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1831401007","https://openalex.org/W1859117663","https://openalex.org/W1935585532","https://openalex.org/W1965863160","https://openalex.org/W1973062929","https://openalex.org/W1975736370","https://openalex.org/W2001576815","https://openalex.org/W2011301426","https://openalex.org/W2020912279","https://openalex.org/W2073026107","https://openalex.org/W2090037139","https://openalex.org/W2097798909","https://openalex.org/W2103315616","https://openalex.org/W2113494828","https://openalex.org/W2114850508","https://openalex.org/W2122277359","https://openalex.org/W2143599753","https://openalex.org/W2146292423","https://openalex.org/W2187138210","https://openalex.org/W2342249984","https://openalex.org/W2401568148","https://openalex.org/W2528263447","https://openalex.org/W2597274540","https://openalex.org/W2599773520","https://openalex.org/W2614144400","https://openalex.org/W2731989040","https://openalex.org/W2737563286","https://openalex.org/W2743137065","https://openalex.org/W2747643030","https://openalex.org/W2757387674","https://openalex.org/W2761461280","https://openalex.org/W2765567136","https://openalex.org/W2888000419","https://openalex.org/W2889474202","https://openalex.org/W2921600473","https://openalex.org/W2946393337","https://openalex.org/W2949421579","https://openalex.org/W2949696308","https://openalex.org/W2950237981","https://openalex.org/W2951322997","https://openalex.org/W2960979937","https://openalex.org/W2973219761","https://openalex.org/W2983176933","https://openalex.org/W2994756760","https://openalex.org/W3003257820","https://openalex.org/W3013167866","https://openalex.org/W3013371767","https://openalex.org/W3027849952","https://openalex.org/W3103145119"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2079089822","https://openalex.org/W2769011817","https://openalex.org/W2362662511","https://openalex.org/W2370701164","https://openalex.org/W2384661423","https://openalex.org/W2523136448","https://openalex.org/W3175942552"],"abstract_inverted_index":{"Coolpup.py":[0],"is":[1,11],"cross-platform,":[2],"open-source":[3],"and":[4,15],"free":[5],"(MIT":[6],"licensed)":[7],"software.":[8],"Source":[9],"code":[10],"available":[12],"from":[13,20],"https://github.com/Phlya/coolpuppy":[14],"it":[16],"can":[17],"be":[18],"installed":[19],"the":[21],"Python":[22],"Packaging":[23],"Index.":[24]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":44},{"year":2024,"cited_by_count":67},{"year":2023,"cited_by_count":35},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":30},{"year":2020,"cited_by_count":12}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2020-02-07T00:00:00"}
