{"id":"https://openalex.org/W7225640427","doi":"https://doi.org/10.1111/2041-210x.70446","title":"ggNetView : An R package for reproducible biological network analysis and visualization","display_name":"ggNetView : An R package for reproducible biological network analysis and visualization","publication_year":2026,"publication_date":"2026-11-09","ids":{"openalex":"https://openalex.org/W7225640427","doi":"https://doi.org/10.1111/2041-210x.70446"},"language":"en","primary_location":{"id":"doi:10.1111/2041-210x.70446","doi":"https://doi.org/10.1111/2041-210x.70446","is_oa":true,"landing_page_url":"https://doi.org/10.1111/2041-210x.70446","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/2041-210x.70446","source":{"id":"https://openalex.org/S1131227","display_name":"Methods in Ecology and Evolution","issn_l":"2041-210X","issn":["2041-210X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-a","jufo-3","ki-jl-2","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"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":"Methods in Ecology and Evolution","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/2041-210x.70446","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5161306859","display_name":"Yue Liu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210110024","display_name":"Institute of Applied Ecology","ror":"https://ror.org/01thb7525","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210110024"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yue Liu","raw_affiliation_strings":["CAS Key Laboratory of Forest Ecology and Silviculture Institute of Applied Ecology, Chinese Academy of Sciences  Shenyang Liaoning China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Forest Ecology and Silviculture Institute of Applied Ecology, Chinese Academy of Sciences  Shenyang Liaoning China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210110024"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100370328","display_name":"Jian Wang","orcid":"https://orcid.org/0000-0001-5184-7023","observed_orcids":["https://orcid.org/0000-0001-5184-7023","https://orcid.org/0000-0002-5756-7505","https://orcid.org/0000-0002-5903-7786"]},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210110024","display_name":"Institute of Applied Ecology","ror":"https://ror.org/01thb7525","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210110024"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chao Wang","raw_affiliation_strings":["CAS Key Laboratory of Forest Ecology and Silviculture Institute of Applied Ecology, Chinese Academy of Sciences  Shenyang Liaoning China"],"raw_orcid":"https://orcid.org/0000-0002-5756-7505","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Forest Ecology and Silviculture Institute of Applied Ecology, Chinese Academy of Sciences  Shenyang Liaoning China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210110024"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100370328"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210110024"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9901999831199646,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9901999831199646,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.002400000113993883,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0017999999690800905,"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/biological-network-visualization","display_name":"biological network visualization","score":0.8769999742507935},{"id":"https://openalex.org/keywords/network-topology-analysis","display_name":"network topology analysis","score":0.9279999732971191},{"id":"https://openalex.org/keywords/network-module-analysis","display_name":"network module analysis","score":0.8090000152587891},{"id":"https://openalex.org/keywords/reproducible-analysis-workflow","display_name":"reproducible analysis workflow","score":0.7639999985694885},{"id":"https://openalex.org/keywords/graph-layout","display_name":"graph layout","score":0.4560000002384186},{"id":"https://openalex.org/keywords/coexpression-network","display_name":"co-expression network","score":0.8309999704360962},{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.9909999966621399},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.7580000162124634}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7342000007629395},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.7060999870300293},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6395000219345093},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.6128000020980835},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6096000075340271},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.5756999850273132},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.5550000071525574},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5318999886512756},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5116999745368958},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4814999997615814},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46320000290870667},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.45350000262260437},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.44909998774528503},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.40779998898506165},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.40630000829696655},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.38609999418258667},{"id":"https://openalex.org/C2911174283","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph Layout","level":4,"score":0.38029998540878296},{"id":"https://openalex.org/C191172861","wikidata":"https://www.wikidata.org/wiki/Q7899321","display_name":"Upstream (networking)","level":2,"score":0.3783000111579895},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.35339999198913574},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3407999873161316},{"id":"https://openalex.org/C2781238097","wikidata":"https://www.wikidata.org/wiki/Q175026","display_name":"Object (grammar)","level":2,"score":0.3212999999523163},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.3160000145435333},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.314300000667572},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.30869999527931213},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.2849000096321106},{"id":"https://openalex.org/C73752529","wikidata":"https://www.wikidata.org/wiki/Q79872","display_name":"Object-oriented programming","level":2,"score":0.2827000021934509},{"id":"https://openalex.org/C139940560","wikidata":"https://www.wikidata.org/wiki/Q290036","display_name":"Network simulation","level":2,"score":0.28110000491142273}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1111/2041-210x.70446","doi":"https://doi.org/10.1111/2041-210x.70446","is_oa":true,"landing_page_url":"https://doi.org/10.1111/2041-210x.70446","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/2041-210x.70446","source":{"id":"https://openalex.org/S1131227","display_name":"Methods in Ecology and Evolution","issn_l":"2041-210X","issn":["2041-210X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-a","jufo-3","ki-jl-2","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"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":"Methods in Ecology and Evolution","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1111/2041-210x.70446","doi":"https://doi.org/10.1111/2041-210x.70446","is_oa":true,"landing_page_url":"https://doi.org/10.1111/2041-210x.70446","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/2041-210x.70446","source":{"id":"https://openalex.org/S1131227","display_name":"Methods in Ecology and Evolution","issn_l":"2041-210X","issn":["2041-210X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-a","jufo-3","ki-jl-2","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"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":"Methods in Ecology and Evolution","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225640427.pdf","grobid_xml":"https://content.openalex.org/works/W7225640427.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1864161604","https://openalex.org/W1966327575","https://openalex.org/W1995054497","https://openalex.org/W2003199491","https://openalex.org/W2011312755","https://openalex.org/W2079201812","https://openalex.org/W2096826541","https://openalex.org/W2113977541","https://openalex.org/W2122184339","https://openalex.org/W2125910575","https://openalex.org/W2148606196","https://openalex.org/W2159675211","https://openalex.org/W2163480486","https://openalex.org/W2236507608","https://openalex.org/W2900569176","https://openalex.org/W2970515629","https://openalex.org/W2990427812","https://openalex.org/W3036634556","https://openalex.org/W4220704002","https://openalex.org/W4282552290","https://openalex.org/W4293661561","https://openalex.org/W4294216483","https://openalex.org/W4310957810","https://openalex.org/W4318218416","https://openalex.org/W4388843329","https://openalex.org/W4391316947","https://openalex.org/W4410967342","https://openalex.org/W4416593451","https://openalex.org/W7161157711","https://openalex.org/W7222941527"],"related_works":["https://openalex.org/W4282552290","https://openalex.org/W4409828964","https://openalex.org/W2071531104","https://openalex.org/W2104843251","https://openalex.org/W3046214778","https://openalex.org/W4411842395","https://openalex.org/W3110476256","https://openalex.org/W7154092274","https://openalex.org/W3211461584","https://openalex.org/W1971425971"],"abstract_inverted_index":{"Abstract":[0],"Biological":[1],"network":[2,31,106,155],"analysis":[3,151],"has":[4,172],"become":[5],"an":[6,29,76],"important":[7],"approach":[8],"for":[9,117],"investigating":[10],"interactions":[11],"among":[12],"microorganisms,":[13],"genes,":[14],"proteins,":[15],"and":[16,22,36,43,57,96,105,121,123,148,156,180,192],"environmental":[17,160,169],"variables":[18,161],"across":[19,54,145],"ecology,":[20],"microbiology,":[21],"molecular":[23],"biology.":[24],"In":[25,67],"practice,":[26],"however,":[27],"turning":[28],"inferred":[30],"into":[32],"a":[33,37,64,81,91,111,131],"clear":[34],"figure":[35],"full":[38],"set":[39,133],"of":[40,93,127,134,142,152],"downstream":[41,98],"topology":[42,101],"module":[44,103],"analyses":[45],"remains":[46],"laborious,":[47],"because":[48],"the":[49,153,188],"required":[50],"steps":[51,99],"are":[52,58,196],"spread":[53],"several":[55],"packages":[56],"often":[59],"finished":[60],"by":[61],"hand":[62],"in":[63],"graphics":[65],"editor.":[66],"response":[68],"to":[69,129,162,175],"these":[70],"challenges,":[71],"we":[72],"have":[73],"developed":[74],"ggNetView,":[75],"R":[77],"package":[78,109,199],"that":[79],"provides":[80],"complete":[82],"analytical":[83],"workflow.":[84],"Its":[85],"upstream":[86],"step":[87],"constructs":[88],"networks":[89,128,147],"from":[90],"variety":[92],"data":[94],"sources,":[95],"its":[97,157],"encompass":[100],"analysis,":[102,104],"visualization.":[107],"The":[108,198],"utilizes":[110],"unified":[112],"graph":[113,190],"object,":[114],"offers":[115],"functions":[116],"geometric":[118],"layout":[119],"construction":[120],"annotation,":[122],"enables":[124,140],"different":[125],"types":[126],"share":[130],"consistent":[132],"aesthetic":[135],"mappings.":[136],"Beyond":[137],"visualization,":[138],"ggNetView":[139,171],"comparison":[141],"similar":[143],"modules":[144,166],"multiple":[146],"supports":[149],"association":[150],"entire":[154],"subnetworks":[158],"with":[159,168,187],"help":[163],"identify":[164],"candidate":[165],"associated":[167],"variables.":[170],"been":[173],"applied":[174],"microbiome":[176],"co\u2010occurrence,":[177],"WGCNA\u2010derived":[178],"co\u2010expression,":[179],"protein\u2013protein":[181],"interaction":[182],"networks.":[183],"Across":[184],"repeated":[185],"runs":[186],"same":[189],"object":[191],"parameters,":[193],"node":[194],"coordinates":[195],"reproduced.":[197],"is":[200],"freely":[201],"available":[202],"at":[203],"https://github.com/Jiawang1209/ggNetView":[204],".":[205]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-10T00:00:00"}
