{"id":"https://openalex.org/W4321373243","doi":"https://doi.org/10.1093/bib/bbad051","title":"FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery","display_name":"FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery","publication_year":2023,"publication_date":"2023-02-17","ids":{"openalex":"https://openalex.org/W4321373243","doi":"https://doi.org/10.1093/bib/bbad051","pmid":"https://pubmed.ncbi.nlm.nih.gov/36806894"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad051","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/bbad051","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040581077","display_name":"Chirag Parsania","orcid":"https://orcid.org/0000-0003-4873-2385"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Chirag Parsania","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau , Macau SAR of China"],"raw_orcid":"https://orcid.org/0000-0003-4873-2385","affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Macau SAR of China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082582375","display_name":"Ruiwen Chen","orcid":"https://orcid.org/0000-0002-8714-0043"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Ruiwen Chen","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau , Macau SAR of China"],"raw_orcid":"https://orcid.org/0000-0001-8780-1078","affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Macau SAR of China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071858110","display_name":"Pooja Sethiya","orcid":"https://orcid.org/0000-0001-6584-3912"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Pooja Sethiya","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau , Macau SAR of China"],"raw_orcid":"https://orcid.org/0000-0001-6584-3912","affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Macau SAR of China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113823434","display_name":"Zhengqiang Miao","orcid":null},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Zhengqiang Miao","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau , Macau SAR of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Macau SAR of China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079806397","display_name":"Liguo Dong","orcid":"https://orcid.org/0000-0002-8805-7487"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Liguo Dong","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau , Macau SAR of China"],"raw_orcid":"https://orcid.org/0000-0002-8805-7487","affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Macau SAR of China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023829717","display_name":"Koon Ho Wong","orcid":"https://orcid.org/0000-0002-9264-5118"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":true,"raw_author_name":"Koon Ho Wong","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau , Macau SAR of China","Institute of Translational Medicine, University of Macau , Macau SAR of China"],"raw_orcid":"https://orcid.org/0000-0002-9264-5118","affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Macau SAR of China","institution_ids":["https://openalex.org/I204512498"]},{"raw_affiliation_string":"Institute of Translational Medicine, University of Macau , Macau SAR of China","institution_ids":["https://openalex.org/I204512498"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5023829717"],"corresponding_institution_ids":["https://openalex.org/I204512498"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.7827,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.84415953,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"2","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":0.9936000108718872,"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":0.9936000108718872,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9918000102043152,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5847892761230469},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5632482171058655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5138952732086182},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.46856266260147095},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41852840781211853},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4109061062335968},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3493086099624634},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3254227936267853},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18661156296730042}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5847892761230469},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5632482171058655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5138952732086182},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.46856266260147095},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41852840781211853},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4109061062335968},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3493086099624634},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3254227936267853},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18661156296730042}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad051","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36806894","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36806894","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10025439","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10025439","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10025439/pdf/bbad051.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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad051","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2763257860","display_name":null,"funder_award_id":"FDCT0033/2021/A1","funder_id":"https://openalex.org/F4320323893","funder_display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia"},{"id":"https://openalex.org/G6388765748","display_name":null,"funder_award_id":"FDCT0099/2022/A2","funder_id":"https://openalex.org/F4320323893","funder_display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia"},{"id":"https://openalex.org/G6564948766","display_name":null,"funder_award_id":"FDCT0106/2020/A","funder_id":"https://openalex.org/F4320323893","funder_display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia"},{"id":"https://openalex.org/G8022726380","display_name":null,"funder_award_id":"MYRG2022-00107-FHS","funder_id":"https://openalex.org/F4320322841","funder_display_name":"Universidade de Macau"}],"funders":[{"id":"https://openalex.org/F4320322841","display_name":"Universidade de Macau","ror":"https://ror.org/01r4q9n85"},{"id":"https://openalex.org/F4320323893","display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia","ror":"https://ror.org/05vna4324"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1885504063","https://openalex.org/W1966755071","https://openalex.org/W1974554923","https://openalex.org/W2035618305","https://openalex.org/W2052375196","https://openalex.org/W2069053494","https://openalex.org/W2086953382","https://openalex.org/W2100305481","https://openalex.org/W2102278945","https://openalex.org/W2103017472","https://openalex.org/W2104005232","https://openalex.org/W2104846587","https://openalex.org/W2121984048","https://openalex.org/W2126700110","https://openalex.org/W2133685961","https://openalex.org/W2140729960","https://openalex.org/W2141595874","https://openalex.org/W2150926065","https://openalex.org/W2152394730","https://openalex.org/W2161793142","https://openalex.org/W2169456326","https://openalex.org/W2171510356","https://openalex.org/W2323326409","https://openalex.org/W2404595262","https://openalex.org/W2527533149","https://openalex.org/W2742478344","https://openalex.org/W2743981571","https://openalex.org/W2896090507","https://openalex.org/W2903808414","https://openalex.org/W2905340019","https://openalex.org/W2912742771","https://openalex.org/W2931264270","https://openalex.org/W2998431554","https://openalex.org/W3029928583","https://openalex.org/W3112600195","https://openalex.org/W3160890790","https://openalex.org/W3204319720","https://openalex.org/W4282942945","https://openalex.org/W6755407716"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2121496884","https://openalex.org/W2387910809","https://openalex.org/W2294221496"],"abstract_inverted_index":{"Bioinformatics":[0],"analysis":[1,34,58,70,125],"and":[2,35,59,72,92,126,145],"visualization":[3,36],"of":[4,50,76,84,133],"high-throughput":[5],"gene":[6,31],"expression":[7,32],"data":[8,33,69,99,107,124,132],"require":[9],"extensive":[10,74],"computer":[11,51],"programming":[12,52],"skills,":[13],"posing":[14],"a":[15],"bottleneck":[16],"for":[17,30,108],"many":[18,66,85],"wet-lab":[19,43,116],"scientists.":[20],"In":[21],"this":[22],"work,":[23],"we":[24],"present":[25],"an":[26,73,109,140,146],"intuitive":[27],"user-friendly":[28],"platform":[29,64,114],"called":[37],"FungiExpresZ.":[38],"FungiExpresZ":[39,113,136],"aims":[40],"to":[41,47,53,118,130],"help":[42],"scientists":[44,117],"with":[45,104],"little":[46],"no":[48],"knowledge":[49],"become":[54],"self-reliant":[55],"in":[56,102,122],"bioinformatics":[57],"generating":[60],"publication-ready":[61],"figures.":[62],"The":[63,112],"contains":[65],"commonly":[67],"used":[68],"tools":[71],"collection":[75],"pre-processed":[77],"public":[78,105],"ribonucleic":[79],"acid":[80],"sequencing":[81],"(RNA-seq)":[82],"datasets":[83],"fungal":[86],"species,":[87],"including":[88],"important":[89],"human,":[90],"plant":[91],"insect":[93],"pathogens.":[94],"Users":[95],"may":[96],"analyse":[97,131],"their":[98,120],"alone":[100],"or":[101],"combination":[103],"RNA-seq":[106],"integrated":[110],"analysis.":[111],"helps":[115],"overcome":[119],"limitations":[121],"genomics":[123],"can":[127],"be":[128],"applied":[129],"any":[134],"organism.":[135],"is":[137],"available":[138],"as":[139],"online":[141],"web-based":[142],"tool":[143],"(https://cparsania.shinyapps.io/FungiExpresZ/)":[144],"offline":[147],"R-Shiny":[148],"package":[149],"(https://github.com/cparsania/FungiExpresZ).":[150]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}
