{"id":"https://openalex.org/W4313312743","doi":"https://doi.org/10.1093/bib/bbac591","title":"bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data","display_name":"bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data","publication_year":2022,"publication_date":"2022-12-05","ids":{"openalex":"https://openalex.org/W4313312743","doi":"https://doi.org/10.1093/bib/bbac591","pmid":"https://pubmed.ncbi.nlm.nih.gov/36583521"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac591","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac591/48782786/bbac591.pdf","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://academic.oup.com/bib/article-pdf/24/1/bbac591/48782786/bbac591.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043288322","display_name":"Ilias Moutsopoulos","orcid":"https://orcid.org/0000-0003-4584-7849"},"institutions":[{"id":"https://openalex.org/I21196054","display_name":"Wellcome/MRC Cambridge Stem Cell Institute","ror":"https://ror.org/05nz0zp31","country_code":"GB","type":"facility","lineage":["https://openalex.org/I21196054","https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I87048295","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ilias Moutsopoulos","raw_affiliation_strings":["Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK","institution_ids":["https://openalex.org/I21196054","https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033998552","display_name":"Eleanor C Williams","orcid":"https://orcid.org/0000-0002-8023-9550"},"institutions":[{"id":"https://openalex.org/I21196054","display_name":"Wellcome/MRC Cambridge Stem Cell Institute","ror":"https://ror.org/05nz0zp31","country_code":"GB","type":"facility","lineage":["https://openalex.org/I21196054","https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I87048295","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Eleanor C Williams","raw_affiliation_strings":["Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK","institution_ids":["https://openalex.org/I21196054","https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053059503","display_name":"Irina Mohorianu","orcid":"https://orcid.org/0000-0003-4863-761X"},"institutions":[{"id":"https://openalex.org/I21196054","display_name":"Wellcome/MRC Cambridge Stem Cell Institute","ror":"https://ror.org/05nz0zp31","country_code":"GB","type":"facility","lineage":["https://openalex.org/I21196054","https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I87048295","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Irina I Mohorianu","raw_affiliation_strings":["Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK"],"raw_orcid":"https://orcid.org/0000-0003-4863-761X","affiliations":[{"raw_affiliation_string":"Wellcome\u2014MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge , CB2 0AW , UK","institution_ids":["https://openalex.org/I21196054","https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053059503"],"corresponding_institution_ids":["https://openalex.org/I21196054","https://openalex.org/I241749"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.6458,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.84205118,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976000189781189,"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/computer-science","display_name":"Computer science","score":0.7714052200317383},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6686223149299622},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6081907749176025},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5619454979896545},{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.49983644485473633},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4912545084953308},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4644909203052521},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44972705841064453},{"id":"https://openalex.org/keywords/exploratory-analysis","display_name":"Exploratory analysis","score":0.4341731071472168},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.43271711468696594},{"id":"https://openalex.org/keywords/modalities","display_name":"Modalities","score":0.4199884831905365},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28781044483184814},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.282254159450531},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0942126214504242}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7714052200317383},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6686223149299622},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6081907749176025},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5619454979896545},{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.49983644485473633},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4912545084953308},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4644909203052521},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44972705841064453},{"id":"https://openalex.org/C3018260909","wikidata":"https://www.wikidata.org/wiki/Q1322871","display_name":"Exploratory analysis","level":2,"score":0.4341731071472168},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.43271711468696594},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.4199884831905365},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28781044483184814},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.282254159450531},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0942126214504242},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C36289849","wikidata":"https://www.wikidata.org/wiki/Q34749","display_name":"Social science","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac591","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac591/48782786/bbac591.pdf","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:36583521","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36583521","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:9851288","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9851288","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac591","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac591/48782786/bbac591.pdf","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":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4300000071525574}],"awards":[{"id":"https://openalex.org/G1618624683","display_name":"Joint Wellcome and MRC Centre, \u2018Wellcome Trust \u2013 Medical Research Council Cambridge Stem Cell Institute\u2019","funder_award_id":"MC_PC_17230","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G2088980218","display_name":null,"funder_award_id":"203151/A/16/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G3078855993","display_name":null,"funder_award_id":"MC_PC_17230","funder_id":"https://openalex.org/F4320314731","funder_display_name":"UK Research and Innovation"},{"id":"https://openalex.org/G6831373058","display_name":null,"funder_award_id":"MC_PC_17230","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7403649556","display_name":null,"funder_award_id":"203151/Z/16/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8872004867","display_name":null,"funder_award_id":"203151/Z/16/Z","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G926432737","display_name":"Cambridge Stem Cell Institute","funder_award_id":"203151","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320314731","display_name":"UK Research and Innovation","ror":"https://ror.org/001aqnf71"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4313312743.pdf","grobid_xml":"https://content.openalex.org/works/W4313312743.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W2076513103","https://openalex.org/W2094011847","https://openalex.org/W2114104545","https://openalex.org/W2120865735","https://openalex.org/W2123364539","https://openalex.org/W2135030836","https://openalex.org/W2138207763","https://openalex.org/W2146053439","https://openalex.org/W2154431984","https://openalex.org/W2159675211","https://openalex.org/W2165909549","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2171808845","https://openalex.org/W2174734928","https://openalex.org/W2179438025","https://openalex.org/W2341539131","https://openalex.org/W2432815617","https://openalex.org/W2583708328","https://openalex.org/W2799170276","https://openalex.org/W2898440040","https://openalex.org/W2903808414","https://openalex.org/W2924358573","https://openalex.org/W2944545583","https://openalex.org/W2949583997","https://openalex.org/W2950402574","https://openalex.org/W2951159620","https://openalex.org/W2952615074","https://openalex.org/W2963367647","https://openalex.org/W2980904816","https://openalex.org/W3093153369","https://openalex.org/W3097582316","https://openalex.org/W3139097098","https://openalex.org/W3164692211","https://openalex.org/W3165530785","https://openalex.org/W3195937479","https://openalex.org/W4221068576","https://openalex.org/W4255156463","https://openalex.org/W6684452758","https://openalex.org/W6761190664","https://openalex.org/W6836575638"],"related_works":["https://openalex.org/W3003271122","https://openalex.org/W2992516105","https://openalex.org/W2381031055","https://openalex.org/W4386721968","https://openalex.org/W2366070815","https://openalex.org/W2360883279","https://openalex.org/W3120899676","https://openalex.org/W3210635025","https://openalex.org/W3198037411","https://openalex.org/W4226120250"],"abstract_inverted_index":{"Bulk":[0],"sequencing":[1],"experiments":[2],"(single-":[3],"and":[4,67,79,92,97],"multi-omics)":[5],"are":[6,44,54],"essential":[7],"for":[8],"exploring":[9],"wide-ranging":[10],"biological":[11,68],"questions.":[12],"To":[13],"facilitate":[14],"interactive,":[15],"exploratory":[16],"tasks,":[17],"coupled":[18],"with":[19,56],"the":[20,39,49],"sharing":[21],"of":[22,48,73,81,94],"easily":[23],"accessible":[24],"information,":[25],"we":[26],"present":[27],"bulkAnalyseR,":[28],"a":[29],"package":[30],"integrating":[31],"state-of-the-art":[32],"approaches":[33],"using":[34],"an":[35],"expression":[36,62,74],"matrix":[37],"as":[38,46],"starting":[40],"point":[41],"(pre-processing":[42],"functions":[43],"available":[45],"part":[47],"package).":[50],"Static":[51],"summary":[52],"images":[53],"replaced":[55],"interactive":[57],"panels":[58],"illustrating":[59],"quality-checking,":[60],"differential":[61],"analysis":[63],"(with":[64],"noise":[65],"detection)":[66],"interpretation":[69],"(enrichment":[70],"analyses,":[71],"identification":[72],"patterns,":[75],"followed":[76],"by":[77],"inference":[78],"comparison":[80,93],"regulatory":[82,99],"interactions).":[83],"bulkAnalyseR":[84],"can":[85],"handle":[86],"different":[87],"modalities,":[88],"facilitating":[89],"robust":[90],"integration":[91],"cis-,":[95],"trans-":[96],"customised":[98],"networks.":[100]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
