{"id":"https://openalex.org/W2883625644","doi":"https://doi.org/10.1093/bioinformatics/bty606","title":"Matt : Unix tools for alternative splicing analysis","display_name":"Matt : Unix tools for alternative splicing analysis","publication_year":2018,"publication_date":"2018-07-13","ids":{"openalex":"https://openalex.org/W2883625644","doi":"https://doi.org/10.1093/bioinformatics/bty606","mag":"2883625644","pmid":"https://pubmed.ncbi.nlm.nih.gov/30010778"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty606","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty606","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072570376","display_name":"Andr\u00e9 Gohr","orcid":"https://orcid.org/0000-0002-8734-7060"},"institutions":[{"id":"https://openalex.org/I4210132884","display_name":"Barcelona Institute of Science and Technology","ror":"https://ror.org/03kpps236","country_code":"ES","type":"education","lineage":["https://openalex.org/I4210132884"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Andr\u00e9 Gohr","raw_affiliation_strings":["Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain","institution_ids":["https://openalex.org/I4210132884","https://openalex.org/I4210137962"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018384674","display_name":"Manuel Irimia","orcid":"https://orcid.org/0000-0002-2179-2567"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I4210132884","display_name":"Barcelona Institute of Science and Technology","ror":"https://ror.org/03kpps236","country_code":"ES","type":"education","lineage":["https://openalex.org/I4210132884"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Manuel Irimia","raw_affiliation_strings":["Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain","Universitat Pompeu Fabra (UPF), Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain","institution_ids":["https://openalex.org/I4210132884","https://openalex.org/I4210137962"]},{"raw_affiliation_string":"Universitat Pompeu Fabra (UPF), Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5018384674","https://openalex.org/A5072570376"],"corresponding_institution_ids":["https://openalex.org/I170486558","https://openalex.org/I4210132884","https://openalex.org/I4210137962"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.694,"has_fulltext":false,"cited_by_count":90,"citation_normalized_percentile":{"value":0.91350098,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"35","issue":"1","first_page":"130","last_page":"132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.961899995803833,"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/T10604","display_name":"RNA Research and Splicing","score":0.961899995803833,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.014100000262260437,"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/T11482","display_name":"RNA modifications and cancer","score":0.0034000000450760126,"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/unix","display_name":"Unix","score":0.8660921454429626},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.613521933555603},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.43397560715675354},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35963666439056396},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2874436676502228},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1967247724533081}],"concepts":[{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.8660921454429626},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.613521933555603},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.43397560715675354},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35963666439056396},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2874436676502228},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1967247724533081}],"mesh":[{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty606","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty606","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30010778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30010778","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:repositori-api.upf.edu:10230/37138","is_oa":false,"landing_page_url":"http://hdl.handle.net/10230/37138","pdf_url":null,"source":{"id":"https://openalex.org/S4306402615","display_name":"Repositori digital de la UPF (Universitat Pompeu Fabra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I170486558","host_organization_name":"Universitat Pompeu Fabra","host_organization_lineage":["https://openalex.org/I170486558"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G2366622498","display_name":null,"funder_award_id":"ERC-StG-LS2-637591","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"},{"id":"https://openalex.org/G5418506387","display_name":null,"funder_award_id":"ERC-AdG-MASCP-670146","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"}],"funders":[{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1965544475","https://openalex.org/W1981963956","https://openalex.org/W2026671856","https://openalex.org/W2034691490","https://openalex.org/W2105694586","https://openalex.org/W2122358139","https://openalex.org/W2375849612","https://openalex.org/W2403981087","https://openalex.org/W2751663599","https://openalex.org/W6713186311"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2033889310","https://openalex.org/W644889988","https://openalex.org/W2086577855","https://openalex.org/W1575418055","https://openalex.org/W189459719","https://openalex.org/W2105855614","https://openalex.org/W1564198055"],"abstract_inverted_index":{"Summary:":[0],"Tracking":[1],"thousands":[2],"of":[3,54,66,82],"alternative":[4],"splicing":[5],"(AS)":[6],"events":[7],"genome-wide":[8],"makes":[9],"their":[10],"downstream":[11],"analysis":[12,75,84],"computationally":[13],"challenging":[14],"and":[15,63,77,95,105,113,117],"laborious.":[16],"Here,":[17],"we":[18],"present":[19],"Matt,":[20],"the":[21,52,64,80],"first":[22],"UNIX":[23],"command-line":[24],"toolkit":[25],"with":[26,102],"focus":[27],"on":[28,120],"high-level":[29,49],"AS":[30,38],"analyses.":[31],"With":[32],"50":[33],"commands":[34],"it":[35],"facilitates":[36],"computational":[37],"analyses":[39],"by":[40,72,86],"(i)":[41],"expediting":[42],"repetitive":[43],"data-preparation":[44],"tasks,":[45],"(ii)":[46],"offering":[47,87],"routine":[48],"analyses,":[50],"including":[51],"extraction":[53],"exon/intron":[55],"features,":[56],"discriminative":[57],"feature":[58],"detection,":[59],"motif":[60,67],"enrichment":[61],"analysis,":[62],"generation":[65],"RNA-maps,":[68],"(iii)":[69],"improving":[70],"reproducibility":[71],"documenting":[73],"all":[74],"steps":[76],"(iv)":[78],"accelerating":[79],"implementation":[81],"own":[83],"pipelines":[85],"users":[88],"to":[89],"exploit":[90],"its":[91,128],"modular":[92],"functionality.":[93],"Availability":[94],"implementation:":[96],"matt.crg.eu":[97],"under":[98],"GNU":[99],"LGPLv3,":[100],"together":[101],"comprehensive":[103],"documentation":[104],"application":[106],"examples.":[107],"Matt":[108],"is":[109],"implemented":[110],"in":[111],"Perl":[112,121],"R,":[114],"invokes":[115],"pdfLATEX":[116],"depends":[118],"only":[119],"Core":[122],"modules/the":[123],"R":[124],"Base":[125],"package":[126],"simplifying":[127],"installation.":[129],"Supplementary":[130,132],"information:":[131],"data":[133],"are":[134],"available":[135],"at":[136],"Bioinformatics":[137],"online.":[138]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":18},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2018-08-03T00:00:00"}
