{"id":"https://openalex.org/W2126669467","doi":"https://doi.org/10.1186/1471-2105-15-81","title":"spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data","display_name":"spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data","publication_year":2014,"publication_date":"2014-03-23","ids":{"openalex":"https://openalex.org/W2126669467","doi":"https://doi.org/10.1186/1471-2105-15-81","mag":"2126669467","pmid":"https://pubmed.ncbi.nlm.nih.gov/24655717"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-81","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-81","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-81","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/counter/pdf/10.1186/1471-2105-15-81","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037239114","display_name":"Kristoffer Vitting\u2010Seerup","orcid":"https://orcid.org/0000-0002-6450-0608"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Kristoffer Vitting-Seerup","raw_affiliation_strings":["Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036161643","display_name":"Bo Porse","orcid":"https://orcid.org/0000-0001-6043-0844"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2802567020","display_name":"Copenhagen University Hospital","ror":"https://ror.org/05bpbnx46","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020"]},{"id":"https://openalex.org/I2802709434","display_name":"Rigshospitalet","ror":"https://ror.org/03mchdq19","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020","https://openalex.org/I2802709434","https://openalex.org/I4210145385"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Bo Torben Porse","raw_affiliation_strings":["Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","The Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"The Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I2802567020","https://openalex.org/I2802709434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026910430","display_name":"Albin Sandelin","orcid":"https://orcid.org/0000-0002-7109-7378"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Albin Sandelin","raw_affiliation_strings":["Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark. albin@binf.ku.dk","Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark. albin@binf.ku.dk","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031574811","display_name":"Johannes Waage","orcid":"https://orcid.org/0000-0002-0603-8822"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2802567020","display_name":"Copenhagen University Hospital","ror":"https://ror.org/05bpbnx46","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020"]},{"id":"https://openalex.org/I2802709434","display_name":"Rigshospitalet","ror":"https://ror.org/03mchdq19","country_code":"DK","type":"healthcare","lineage":["https://openalex.org/I2802567020","https://openalex.org/I2802709434","https://openalex.org/I4210145385"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Johannes Waage","raw_affiliation_strings":["Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","The Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK-2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"The Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I2802567020","https://openalex.org/I2802709434"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5026910430","https://openalex.org/A5031574811"],"corresponding_institution_ids":["https://openalex.org/I124055696","https://openalex.org/I2802567020","https://openalex.org/I2802709434"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":4.8436,"has_fulltext":true,"cited_by_count":119,"citation_normalized_percentile":{"value":0.96144223,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"15","issue":"1","first_page":"81","last_page":"81"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/rna-seq","display_name":"RNA-Seq","score":0.7084285020828247},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.6249850988388062},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5922357439994812},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.516936719417572},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.46976184844970703},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4540844261646271},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39806774258613586},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38269463181495667},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3598122000694275},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32819271087646484},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31517377495765686},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2324512004852295},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.22681090235710144},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1752769649028778},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09465715289115906},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06347528100013733},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.062137484550476074}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7084285020828247},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.6249850988388062},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5922357439994812},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.516936719417572},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.46976184844970703},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4540844261646271},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39806774258613586},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38269463181495667},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3598122000694275},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32819271087646484},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31517377495765686},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2324512004852295},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.22681090235710144},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1752769649028778},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09465715289115906},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06347528100013733},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.062137484550476074}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D007438","descriptor_name":"Introns","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","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":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D045325","descriptor_name":"HCT116 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045325","descriptor_name":"HCT116 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045325","descriptor_name":"HCT116 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-15-81","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-81","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-81","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:24655717","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24655717","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2975722","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3998036","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/af1a890d-5abc-4c9a-990c-472c3721e8cc","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/af1a890d-5abc-4c9a-990c-472c3721e8cc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Vitting-Seerup , K , Porse , B T , Sandelin , A & Waage , J 2014 , ' spliceR : an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data ' , B M C Bioinformatics , vol. 15 , 81 , pp. 1-7 . https://doi.org/10.1186/1471-2105-15-81","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-81","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-81","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-81","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":[],"awards":[{"id":"https://openalex.org/G8101383944","display_name":null,"funder_award_id":"R82-2010-6779","funder_id":"https://openalex.org/F4320321999","funder_display_name":"Lundbeckfonden"}],"funders":[{"id":"https://openalex.org/F4320320337","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53"},{"id":"https://openalex.org/F4320321999","display_name":"Lundbeckfonden","ror":"https://ror.org/03hz8wd80"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320327918","display_name":"H. Lundbeck A/S","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2126669467.pdf","grobid_xml":"https://content.openalex.org/works/W2126669467.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1966833356","https://openalex.org/W1986456492","https://openalex.org/W1989367702","https://openalex.org/W1990848127","https://openalex.org/W2011920499","https://openalex.org/W2015207840","https://openalex.org/W2046583421","https://openalex.org/W2048194168","https://openalex.org/W2086804751","https://openalex.org/W2103635790","https://openalex.org/W2103823493","https://openalex.org/W2105402655","https://openalex.org/W2107730196","https://openalex.org/W2112954412","https://openalex.org/W2114104545","https://openalex.org/W2117677974","https://openalex.org/W2123402634","https://openalex.org/W2139795130","https://openalex.org/W2141458291","https://openalex.org/W2141885858","https://openalex.org/W2146970739","https://openalex.org/W2151462466","https://openalex.org/W2152239989","https://openalex.org/W2157560322","https://openalex.org/W2159730169","https://openalex.org/W2160697532","https://openalex.org/W2163516449","https://openalex.org/W2916251779","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W4394426846","https://openalex.org/W4224241862","https://openalex.org/W4200033037","https://openalex.org/W4394543623","https://openalex.org/W4410026407","https://openalex.org/W2889547007","https://openalex.org/W1510729279","https://openalex.org/W3213655218","https://openalex.org/W4394560977","https://openalex.org/W2119034410"],"abstract_inverted_index":{"BACKGROUND:":[0],"RNA-seq":[1,54,145,156],"data":[2],"is":[3,10,136,159,166],"currently":[4],"underutilized,":[5],"in":[6,24],"part":[7],"because":[8],"it":[9],"difficult":[11],"to":[12,30,56,109],"predict":[13],"the":[14,49,89,93,118,124,142,170],"functional":[15],"impact":[16],"of":[17,38,43,83,92,131,144,153,155],"alternate":[18],"transcription":[19],"events.":[20,80],"Recent":[21],"software":[22],"improvements":[23],"full-length":[25,50],"transcript":[26,51,103,111],"deconvolution":[27],"prompted":[28],"us":[29],"develop":[31],"spliceR,":[32],"an":[33,137,162],"R":[34,163],"package":[35,164],"for":[36],"classification":[37],"alternative":[39,63,70],"splicing":[40],"and":[41,65,76,146,165],"prediction":[42],"coding":[44,119],"potential.":[45],"RESULTS:":[46],"spliceR":[47,86,116,135,158],"uses":[48],"output":[52],"from":[53,169],"assemblers":[55],"detect":[57],"single":[58],"or":[59,72],"multiple":[60],"exon":[61,74,79],"skipping,":[62],"donor":[64],"acceptor":[66],"sites,":[67],"intron":[68],"retention,":[69],"first":[71],"last":[73],"usage,":[75],"mutually":[77],"exclusive":[78],"For":[81,101],"each":[82,102,132],"these":[84],"events":[85],"also":[87],"annotates":[88],"genomic":[90],"coordinates":[91],"differentially":[94],"spliced":[95],"elements,":[96],"facilitating":[97],"downstream":[98],"sequence":[99],"analysis.":[100],"isoform":[104],"fraction":[105],"values":[106],"are":[107],"calculated":[108],"identify":[110],"switching":[112],"between":[113],"conditions.":[114],"Lastly,":[115],"predicts":[117],"potential,":[120],"as":[121,123,161],"well":[122],"potential":[125],"nonsense":[126],"mediated":[127],"decay":[128],"(NMD)":[129],"sensitivity":[130],"transcript.":[133],"CONCLUSIONS:":[134],"easy-to-use":[138],"tool":[139],"that":[140],"extends":[141],"usability":[143],"assembly":[147],"technologies":[148],"by":[149],"allowing":[150],"greater":[151],"depth":[152],"annotation":[154],"data.":[157],"implemented":[160],"freely":[167],"available":[168],"Bioconductor":[171],"repository":[172],"(":[173],"http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html).":[174]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-10-10T00:00:00"}