{"id":"https://openalex.org/W3195937479","doi":"https://doi.org/10.1186/s12859-021-04321-2","title":"Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts","display_name":"Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts","publication_year":2021,"publication_date":"2021-08-19","ids":{"openalex":"https://openalex.org/W3195937479","doi":"https://doi.org/10.1186/s12859-021-04321-2","mag":"3195937479","pmid":"https://pubmed.ncbi.nlm.nih.gov/34412594"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04321-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04321-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04321-2","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/track/pdf/10.1186/s12859-021-04321-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039357231","display_name":"John Cole","orcid":"https://orcid.org/0000-0002-6386-766X"},"institutions":[{"id":"https://openalex.org/I4210094430","display_name":"Wellcome Centre for Molecular Parasitology","ror":"https://ror.org/00m7w8s72","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210094430","https://openalex.org/I7882870","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"John J. Cole","raw_affiliation_strings":["GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK. John.Cole@glasgow.ac.uk","Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK. John.Cole@glasgow.ac.uk","Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK"],"raw_orcid":"https://orcid.org/0000-0002-6386-766X","affiliations":[{"raw_affiliation_string":"GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK. John.Cole@glasgow.ac.uk","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK. John.Cole@glasgow.ac.uk","institution_ids":["https://openalex.org/I7882870","https://openalex.org/I4210094430"]},{"raw_affiliation_string":"Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088113370","display_name":"Bekir A. Faydaci","orcid":"https://orcid.org/0000-0002-8304-7669"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Bekir A. Faydaci","raw_affiliation_strings":["Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021829305","display_name":"David McGuinness","orcid":"https://orcid.org/0000-0003-2947-2047"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David McGuinness","raw_affiliation_strings":["Glasgow Polyomics, Wolfson-Wohl Building, University of Glasgow, Garscube Estate, Glasgow, G61 1BD, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Glasgow Polyomics, Wolfson-Wohl Building, University of Glasgow, Garscube Estate, Glasgow, G61 1BD, Scotland, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002606469","display_name":"Robin Shaw","orcid":"https://orcid.org/0000-0001-5503-5233"},"institutions":[{"id":"https://openalex.org/I4210143228","display_name":"Cancer Research UK Scotland Institute","ror":"https://ror.org/03pv69j64","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801316944","https://openalex.org/I4210143228"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Robin Shaw","raw_affiliation_strings":["Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, Glasgow, G61 1BD, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, Glasgow, G61 1BD, Scotland, UK","institution_ids":["https://openalex.org/I4210143228","https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051609124","display_name":"Rose A. Maciewicz","orcid":"https://orcid.org/0000-0002-5371-7828"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rose A. Maciewicz","raw_affiliation_strings":["GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK","Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK","institution_ids":[]},{"raw_affiliation_string":"Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003068372","display_name":"Neil Robertson","orcid":"https://orcid.org/0000-0002-9509-1157"},"institutions":[{"id":"https://openalex.org/I4210143228","display_name":"Cancer Research UK Scotland Institute","ror":"https://ror.org/03pv69j64","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801316944","https://openalex.org/I4210143228"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Neil A. Robertson","raw_affiliation_strings":["Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, Glasgow, G61 1BD, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, Glasgow, G61 1BD, Scotland, UK","institution_ids":["https://openalex.org/I4210143228","https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028761875","display_name":"Carl S. Goodyear","orcid":"https://orcid.org/0000-0001-5926-5941"},"institutions":[{"id":"https://openalex.org/I4210094430","display_name":"Wellcome Centre for Molecular Parasitology","ror":"https://ror.org/00m7w8s72","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210094430","https://openalex.org/I7882870","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Carl S. Goodyear","raw_affiliation_strings":["GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK. Carl.Goodyear@glasgow.ac.uk","Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK. Carl.Goodyear@glasgow.ac.uk","GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK. Carl.Goodyear@glasgow.ac.uk","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK. Carl.Goodyear@glasgow.ac.uk","institution_ids":["https://openalex.org/I7882870","https://openalex.org/I4210094430"]},{"raw_affiliation_string":"GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5039357231"],"corresponding_institution_ids":["https://openalex.org/I4210094430","https://openalex.org/I7882870"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.1167,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.88201719,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"411","last_page":"411"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7523000240325928,"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":0.7523000240325928,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.057500001043081284,"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/T10066","display_name":"Gut microbiota and health","score":0.017000000923871994,"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/scripting-language","display_name":"Scripting language","score":0.7138102650642395},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.70389324426651},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6614205241203308},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5872294306755066},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5872206687927246},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.5092412233352661},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.4587010145187378},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45170533657073975},{"id":"https://openalex.org/keywords/fidelity","display_name":"Fidelity","score":0.4468207061290741},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4196997582912445},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2617783546447754},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20861393213272095},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10463741421699524}],"concepts":[{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7138102650642395},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.70389324426651},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6614205241203308},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5872294306755066},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5872206687927246},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.5092412233352661},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.4587010145187378},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45170533657073975},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.4468207061290741},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4196997582912445},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2617783546447754},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20861393213272095},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10463741421699524},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome 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":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","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":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04321-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04321-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04321-2","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:34412594","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34412594","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:eprints.gla.ac.uk:249966","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:doaj.org/article:9bca106272ef4240bc9afd063a856c67","is_oa":true,"landing_page_url":"https://doaj.org/article/9bca106272ef4240bc9afd063a856c67","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 22, Iss 1, Pp 1-21 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8375142","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8375142","pdf_url":null,"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"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04321-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04321-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04321-2","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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6100000143051147}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3195937479.pdf","grobid_xml":"https://content.openalex.org/works/W3195937479.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W2043221884","https://openalex.org/W2103017472","https://openalex.org/W2114104545","https://openalex.org/W2118258530","https://openalex.org/W2129497875","https://openalex.org/W2130410032","https://openalex.org/W2135253885","https://openalex.org/W2151014102","https://openalex.org/W2159482845","https://openalex.org/W2160697532","https://openalex.org/W2162143298","https://openalex.org/W2162816478","https://openalex.org/W2167321137","https://openalex.org/W2169456326","https://openalex.org/W2179438025","https://openalex.org/W2222859485","https://openalex.org/W2228647225","https://openalex.org/W2230749025","https://openalex.org/W2233603983","https://openalex.org/W2235443461","https://openalex.org/W2236822143","https://openalex.org/W2323326409","https://openalex.org/W2403934794","https://openalex.org/W2412914653","https://openalex.org/W2513453485","https://openalex.org/W2577896867","https://openalex.org/W2770331207","https://openalex.org/W2781939187","https://openalex.org/W2799170276","https://openalex.org/W2900569176","https://openalex.org/W2917207851","https://openalex.org/W2949583997","https://openalex.org/W2951912016","https://openalex.org/W2952499863","https://openalex.org/W3118495573","https://openalex.org/W3169609444","https://openalex.org/W4250359879","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1970117064","https://openalex.org/W1787170397","https://openalex.org/W4292347844"],"abstract_inverted_index":{"BACKGROUND:":[0],"Once":[1],"bulk":[2,76,155,165,207],"RNA-seq":[3,77,156,166,208],"data":[4],"has":[5],"been":[6],"processed,":[7],"i.e.":[8],"aligned":[9],"and":[10,13,28,36,45,47,56,79,87,95,115,126,142,195,202,220],"then":[11],"expression":[12],"differential":[14,102],"tables":[15],"generated,":[16],"there":[17],"remains":[18],"the":[19,23,31,92,170,200],"essential":[20],"process":[21],"where":[22],"biology":[24],"is":[25,48,214],"explored,":[26],"visualized":[27],"interpreted.":[29],"Without":[30],"use":[32],"of":[33,106,121,172],"a":[34,73,84,127,147,153,183],"visualisation":[35,55,78],"interpretation":[37,57,80],"pipeline":[38],"this":[39],"step":[40],"can":[41,160,198],"be":[42,161],"time":[43,201],"consuming":[44],"laborious,":[46],"often":[49],"completed":[50],"using":[51],"R.":[52],"Though":[53],"commercial":[54],"pipelines":[58,63,193],"are":[59,64],"comprehensive,":[60],"freely":[61,74,191],"available":[62,75,192],"currently":[65],"more":[66],"limited.":[67],"RESULTS:":[68],"Here":[69],"we":[70],"demonstrate":[71,145],"Searchlight,":[72],"pipeline.":[81],"Searchlight":[82,133,159,197,213],"provides:":[83],"comprehensive":[85],"statistical":[86],"visual":[88],"analysis,":[89],"focusing":[90],"on":[91],"global,":[93],"pathway":[94],"single":[96],"gene":[97],"levels;":[98],"compatibility":[99],"with":[100],"most":[101],"experimental":[103,109],"designs":[104],"irrespective":[105],"organism":[107],"or":[108,188],"complexity,":[110],"via":[111,123],"three":[112],"workflows;":[113],"reports;":[114],"support":[116],"for":[117,216],"downstream":[118],"user":[119],"modification":[120],"plots":[122],"user-friendly":[124],"R-scripts":[125],"Shiny":[128],"app.":[129],"We":[130,144],"show":[131],"that":[132,151],"offers":[134],"greater":[135],"automation":[136],"than":[137],"current":[138,189],"best":[139,190],"tools":[140],"(VIPER":[141,194],"BioJupies).":[143],"in":[146,176],"timed":[148],"re-analysis":[149],"study,":[150],"alongside":[152],"standard":[154],"processing":[157],"pipeline,":[158],"used":[162],"to":[163,169,182,205,210],"complete":[164,206],"projects":[167,209],"up":[168],"point":[171],"manuscript":[173,211],"quality":[174],"figures,":[175],"under":[177],"3":[178],"h.":[179],"CONCLUSIONS:":[180],"Compared":[181],"manual":[184],"R":[185],"based":[186],"analysis":[187],"BioJupies),":[196],"reduce":[199],"effort":[203],"needed":[204],"level.":[212],"suitable":[215],"bioinformaticians,":[217],"service":[218],"providers":[219],"bench":[221],"scientists.":[222],"https://github.com/Searchlight2/Searchlight2":[223],".":[224]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}
