{"id":"https://openalex.org/W4404508958","doi":"https://doi.org/10.1093/bioinformatics/btae695","title":"Damsel: analysis and visualisation of DamID sequencing in R","display_name":"Damsel: analysis and visualisation of DamID sequencing in R","publication_year":2024,"publication_date":"2024-11-18","ids":{"openalex":"https://openalex.org/W4404508958","doi":"https://doi.org/10.1093/bioinformatics/btae695","pmid":"https://pubmed.ncbi.nlm.nih.gov/39558607"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae695","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae695","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101631759","display_name":"Caitlin G Page","orcid":"https://orcid.org/0009-0004-7949-8143"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Caitlin G Page","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, 3000,","Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, 3000,","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029168954","display_name":"Andrew Lonsdale","orcid":"https://orcid.org/0000-0002-0292-2880"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]},{"id":"https://openalex.org/I4210150290","display_name":"Murdoch Children's Research Institute","ror":"https://ror.org/048fyec77","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I4210150290"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Andrew Lonsdale","raw_affiliation_strings":["Murdoch Children\u2019s Research Institute , Parkville, 3052,","Peter MacCallum Cancer Centre , Melbourne, 3000,","Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,","Murdoch Children's Research Institute, Parkville, VIC 3052, Australia"],"affiliations":[{"raw_affiliation_string":"Murdoch Children\u2019s Research Institute , Parkville, 3052,","institution_ids":["https://openalex.org/I4210150290"]},{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, 3000,","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Murdoch Children's Research Institute, Parkville, VIC 3052, Australia","institution_ids":["https://openalex.org/I4210150290"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028792799","display_name":"Katrina A. Mitchell","orcid":null},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Katrina A Mitchell","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, 3000,","Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, 3000,","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108605263","display_name":"Jan Schr\u00f6der","orcid":"https://orcid.org/0000-0001-5270-0605"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210105123","display_name":"Peter Doherty Institute","ror":"https://ror.org/016899r71","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1320473756","https://openalex.org/I165779595","https://openalex.org/I4210105123","https://openalex.org/I4210158168"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jan Schr\u00f6der","raw_affiliation_strings":["Computational Sciences Initiative, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, 3000,"],"affiliations":[{"raw_affiliation_string":"Computational Sciences Initiative, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, 3000,","institution_ids":["https://openalex.org/I4210105123","https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022412897","display_name":"Kieran F. Harvey","orcid":"https://orcid.org/0000-0001-7845-369X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Kieran F Harvey","raw_affiliation_strings":["Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University , Clayton, 3800,","Peter MacCallum Cancer Centre , Melbourne, 3000,","Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,"],"affiliations":[{"raw_affiliation_string":"Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University , Clayton, 3800,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, 3000,","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066632434","display_name":"Alicia Oshlack","orcid":"https://orcid.org/0000-0001-9788-5690"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Alicia Oshlack","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, 3000,","School of Mathematics and Statistics, The University of Melbourne , Parkville, 3010,","Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, 3000,","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"School of Mathematics and Statistics, The University of Melbourne , Parkville, 3010,","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, The University of Melbourne , Parkville, 3010,","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101631759"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.229,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.58956518,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"40","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.983299970626831,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.983299970626831,"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/visualization","display_name":"Visualization","score":0.6898581981658936},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5659201145172119},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.35929763317108154},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3143676519393921}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6898581981658936},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5659201145172119},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.35929763317108154},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3143676519393921}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae695","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:39558607","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39558607","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:11604169","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11604169","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11604169/pdf/btae695.pdf","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/btae695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae695","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"awards":[{"id":"https://openalex.org/G1050039735","display_name":null,"funder_award_id":"APP1194467","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G273974938","display_name":null,"funder_award_id":"1196256","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G4880539169","display_name":null,"funder_award_id":"1194467","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G8905844459","display_name":null,"funder_award_id":"APP11","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1573323739","https://openalex.org/W2072420737","https://openalex.org/W2072551458","https://openalex.org/W2107018762","https://openalex.org/W2107060225","https://openalex.org/W2114104545","https://openalex.org/W2114709909","https://openalex.org/W2130116522","https://openalex.org/W2158226173","https://openalex.org/W2161117954","https://openalex.org/W2261235911","https://openalex.org/W2466314544","https://openalex.org/W2500825507","https://openalex.org/W2899775893","https://openalex.org/W2922042625","https://openalex.org/W2950464315","https://openalex.org/W4241872665","https://openalex.org/W4254687493","https://openalex.org/W4385698665","https://openalex.org/W4391166655"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2068608913","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W3204019825"],"abstract_inverted_index":{"The":[0],"R":[1],"package":[2],"Damsel":[3],"is":[4,16],"available":[5,17],"for":[6],"install":[7],"through":[8],"the":[9,14],"Bioconductor":[10],"project":[11],"https://bioconductor.org/packages/release/bioc/html/Damsel.html":[12],"and":[13],"code":[15],"on":[18],"GitHub":[19],"https://github.com/Oshlack/Damsel/.":[20]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
