{"id":"https://openalex.org/W4385698665","doi":"https://doi.org/10.1186/s12859-023-05438-2","title":"ggcoverage: an R package to visualize and annotate genome coverage for various NGS data","display_name":"ggcoverage: an R package to visualize and annotate genome coverage for various NGS data","publication_year":2023,"publication_date":"2023-08-09","ids":{"openalex":"https://openalex.org/W4385698665","doi":"https://doi.org/10.1186/s12859-023-05438-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/37559015"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05438-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05438-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05438-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05438-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013296463","display_name":"Yabing Song","orcid":"https://orcid.org/0000-0003-1352-2994"},"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":"Yabing Song","raw_affiliation_strings":["School of Life Sciences, Tsinghua University, Beijing, China. songyb18@mails.tsinghua.edu.cn","School of Life Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Tsinghua University, Beijing, China. songyb18@mails.tsinghua.edu.cn","institution_ids":[]},{"raw_affiliation_string":"School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100619210","display_name":"Jianbin Wang","orcid":"https://orcid.org/0000-0001-6725-7925"},"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":"Jianbin Wang","raw_affiliation_strings":["School of Life Sciences, Tsinghua University, Beijing, China. jianbinwang@tsinghua.edu.cn","School of Life Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Tsinghua University, Beijing, China. jianbinwang@tsinghua.edu.cn","institution_ids":[]},{"raw_affiliation_string":"School of Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013296463"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":4.0029,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.94256146,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"1","first_page":"309","last_page":"309"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7225000262260437,"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":0.7225000262260437,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.04619999974966049,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.023900000378489494,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/computer-science","display_name":"Computer science","score":0.790921688079834},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7365034818649292},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6304354071617126},{"id":"https://openalex.org/keywords/personalization","display_name":"Personalization","score":0.5425392389297485},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.5322693586349487},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.5022237300872803},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4961851239204407},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.45947402715682983},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42489057779312134},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.40048763155937195},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.400422602891922},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2694857120513916},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12022155523300171},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11297369003295898},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10537710785865784},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.10472747683525085}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.790921688079834},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7365034818649292},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6304354071617126},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.5425392389297485},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.5322693586349487},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.5022237300872803},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4961851239204407},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.45947402715682983},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42489057779312134},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.40048763155937195},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.400422602891922},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2694857120513916},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12022155523300171},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11297369003295898},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10537710785865784},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.10472747683525085},{"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":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05438-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05438-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05438-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37559015","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37559015","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10413535","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10413535","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10413535/pdf/12859_2023_Article_5438.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c2de7f24c26747a89fdb76d5d866a1dc","is_oa":true,"landing_page_url":"https://doaj.org/article/c2de7f24c26747a89fdb76d5d866a1dc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-7 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05438-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05438-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05438-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8721784949","display_name":null,"funder_award_id":"22050004","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"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385698665.pdf"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2021341670","https://openalex.org/W2030710966","https://openalex.org/W2072420737","https://openalex.org/W2104836314","https://openalex.org/W2128016314","https://openalex.org/W2171111703","https://openalex.org/W2236822143","https://openalex.org/W2341539131","https://openalex.org/W2411397641","https://openalex.org/W2415505014","https://openalex.org/W2952527196","https://openalex.org/W2985066411","https://openalex.org/W4254687493","https://openalex.org/W4399648717"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2429057255","https://openalex.org/W2187546663","https://openalex.org/W148745890","https://openalex.org/W4389670110","https://openalex.org/W4205801320"],"abstract_inverted_index":{"BACKGROUND:":[0],"Visualizing":[1],"genome":[2,18,20,38,90,199],"coverage":[3,39,91,200],"is":[4,47,208],"of":[5,92,182,201],"vital":[6],"importance":[7],"to":[8,36,54,86,119,138,140,195],"inspect":[9],"and":[10,40,45,69,71,88,94,107,116,126,148,166,180,192,197,203,216],"interpret":[11],"various":[12,135],"next-generation":[13],"sequencing":[14],"(NGS)":[15],"data.":[16],"Besides":[17],"coverage,":[19],"annotations":[21,43,137,152],"are":[22,61,219],"also":[23],"crucial":[24],"in":[25,103],"the":[26,42,72,150,170,178,213,217],"visualization.":[27],"While":[28],"different":[29,33,141],"NGS":[30,142],"data":[31,128,143],"require":[32],"annotations,":[34,70],"how":[35],"visualize":[37,87,196],"add":[41],"appropriately":[44],"conveniently":[46],"challenging.":[48],"Many":[49],"tools":[50,60],"have":[51],"been":[52],"developed":[53],"address":[55],"this":[56],"issue.":[57],"However,":[58],"existing":[59],"often":[62],"inflexible,":[63],"complicated,":[64],"lack":[65],"necessary":[66],"preprocessing":[67],"steps":[68],"figures":[73],"generated":[74],"support":[75],"limited":[76],"customization.":[77],"RESULTS:":[78],"Here,":[79],"we":[80],"introduce":[81],"ggcoverage,":[82],"an":[83],"R":[84],"package":[85,207],"annotate":[89,198],"multi-groups":[93,202],"multi-omics.":[95,204],"The":[96,205],"input":[97],"files":[98],"for":[99],"ggcoverage":[100,113,133,161,176,186,206],"can":[101,153,162,168],"be":[102,154],"BAM,":[104],"BigWig,":[105],"BedGraph":[106],"TSV":[108],"formats.":[109],"For":[110],"better":[111],"usability,":[112],"provides":[114,134,187],"reliable":[115],"efficient":[117,191],"ways":[118],"perform":[120],"read":[121],"normalization,":[122],"consensus":[123],"peaks":[124],"generation":[125],"track":[127],"loading":[129],"with":[130,157,172],"state-of-the-art":[131],"tools.":[132],"available":[136,151,209,220],"adapt":[139],"(e.g.":[144],"WGS/WES,":[145],"RNA-seq,":[146],"ChIP-seq)":[147],"all":[149],"easily":[155],"superimposed":[156],"'":[158],"+":[159],"'.":[160],"generate":[163],"publication-quality":[164],"plots":[165,171],"users":[167],"customize":[169],"ggplot2.":[173],"In":[174],"addition,":[175],"supports":[177],"visualization":[179],"annotation":[181],"protein":[183],"coverage.":[184],"CONCLUSIONS:":[185],"a":[188],"flexible,":[189],"programmable,":[190],"user-friendly":[193],"way":[194],"at":[210,221],"https://github.com/showteeth/ggcoverage":[211],"under":[212],"MIT":[214],"license,":[215],"vignettes":[218],"https://showteeth.github.io/ggcoverage/":[222],".":[223]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":11}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
