{"id":"https://openalex.org/W1877042322","doi":"https://doi.org/10.1093/bioinformatics/btv436","title":"Designing alternative splicing RNA-seq studies. Beyond generic guidelines","display_name":"Designing alternative splicing RNA-seq studies. Beyond generic guidelines","publication_year":2015,"publication_date":"2015-07-27","ids":{"openalex":"https://openalex.org/W1877042322","doi":"https://doi.org/10.1093/bioinformatics/btv436","mag":"1877042322","pmid":"https://pubmed.ncbi.nlm.nih.gov/26220961"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv436","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv436","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3631/17122760/btv436.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3631/17122760/btv436.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085139761","display_name":"Camille Stephan\u2010Otto Attolini","orcid":"https://orcid.org/0000-0001-8045-320X"},"institutions":[{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Camille Stephan-Otto Attolini","raw_affiliation_strings":["1 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain,","institution_ids":["https://openalex.org/I4210122345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035916095","display_name":"V\u00edctor Pe\u00f1a","orcid":"https://orcid.org/0000-0002-3801-5203"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Victor Pe\u00f1a","raw_affiliation_strings":["2 Department of Statistical Science, Duke University, Durham, North Carolina, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Statistical Science, Duke University, Durham, North Carolina, USA and","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063900043","display_name":"David Rossell","orcid":"https://orcid.org/0000-0002-7104-5789"},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David Rossell","raw_affiliation_strings":["3 Department of Statistics, University of Warwick, Coventry, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Statistics, University of Warwick, Coventry, UK","institution_ids":["https://openalex.org/I39555362"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085139761"],"corresponding_institution_ids":["https://openalex.org/I4210122345"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9034,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.7387377,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"31","issue":"22","first_page":"3631","last_page":"3637"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.3492000102996826,"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":0.3492000102996826,"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":0.298799991607666,"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":0.20329999923706055,"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/bioconductor","display_name":"Bioconductor","score":0.7971128225326538},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7684098482131958},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5115472078323364},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5054624080657959},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.47651708126068115},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.43962469696998596},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4260387122631073},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4090338349342346},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3602241575717926},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.326957106590271},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2409418225288391},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11407363414764404},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10237258672714233},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.08974951505661011}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.7971128225326538},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7684098482131958},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5115472078323364},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5054624080657959},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.47651708126068115},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.43962469696998596},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4260387122631073},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4090338349342346},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3602241575717926},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.326957106590271},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2409418225288391},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11407363414764404},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10237258672714233},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.08974951505661011},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":"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":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv436","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv436","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3631/17122760/btv436.pdf","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:26220961","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26220961","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":null},{"id":"pmh:oai:upcommons.upc.edu:2117/430247","is_oa":false,"landing_page_url":"https://hdl.handle.net/2117/430247","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"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"},{"id":"pmh:oai:europepmc.org:4045391","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4757954","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/22/3631","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/22/3631","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv436","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv436","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3631/17122760/btv436.pdf","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"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.41999998688697815,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1882219601","https://openalex.org/W1966923966","https://openalex.org/W1974575979","https://openalex.org/W1988520084","https://openalex.org/W1999574084","https://openalex.org/W2019595176","https://openalex.org/W2025943989","https://openalex.org/W2038492487","https://openalex.org/W2051486134","https://openalex.org/W2053057991","https://openalex.org/W2054576015","https://openalex.org/W2068568257","https://openalex.org/W2070494252","https://openalex.org/W2087001748","https://openalex.org/W2089357254","https://openalex.org/W2090079179","https://openalex.org/W2096173343","https://openalex.org/W2100305481","https://openalex.org/W2108234281","https://openalex.org/W2110065044","https://openalex.org/W2118017981","https://openalex.org/W2124715997","https://openalex.org/W2126398084","https://openalex.org/W2137526110","https://openalex.org/W2149696065","https://openalex.org/W2156631105","https://openalex.org/W2160235457","https://openalex.org/W2161318011","https://openalex.org/W2166820820","https://openalex.org/W2168963004","https://openalex.org/W2169456326","https://openalex.org/W2259938310","https://openalex.org/W2974222084","https://openalex.org/W3098034577","https://openalex.org/W3105872783","https://openalex.org/W3122121132"],"related_works":["https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W3156537409","https://openalex.org/W2140163842","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2133055377","https://openalex.org/W2287365612","https://openalex.org/W2121792613"],"abstract_inverted_index":{"MOTIVATION:":[0],"Designing":[1],"an":[2],"RNA-seq":[3],"study":[4,99],"depends":[5],"critically":[6],"on":[7,42],"its":[8],"specific":[9],"goals,":[10],"technology":[11],"and":[12,34,55,64,104,107,139],"underlying":[13],"biology,":[14],"which":[15],"renders":[16],"general":[17],"guidelines":[18],"inadequate.":[19],"We":[20,46,124],"propose":[21],"a":[22,40],"Bayesian":[23],"framework":[24,94,130],"to":[25,73,109],"customize":[26],"experiments":[27],"so":[28],"that":[29,119],"goals":[30],"can":[31,131,140],"be":[32,132],"attained":[33],"resources":[35],"are":[36,168],"not":[37],"wasted,":[38],"with":[39,134],"focus":[41],"alternative":[43],"splicing.":[44],"RESULTS:":[45],"studied":[47],"how":[48,108],"read":[49],"length,":[50],"sequencing":[51],"depth,":[52],"library":[53],"preparation":[54],"the":[56,74,102,129,159],"number":[57],"of":[58,62],"replicates":[59],"affects":[60],"cost-effectiveness":[61],"single-sample":[63],"group":[65],"comparison":[66],"studies.":[67],"Optimal":[68],"settings":[69],"varied":[70],"strongly":[71],"according":[72],"target":[75],"organism":[76],"or":[77],"tissue":[78],"(potential":[79],"50-500%":[80],"cost":[81],"cuts)":[82],"and,":[83],"interestingly,":[84],"short":[85],"reads":[86,89],"outperformed":[87],"long":[88],"for":[90,98,122],"standard":[91],"analyses.":[92],"Our":[93],"learns":[95],"key":[96],"characteristics":[97],"design":[100],"from":[101],"data,":[103],"predicts":[105],"if":[106],"continue":[110],"experimentation.":[111],"These":[112],"predictions":[113],"matched":[114],"several":[115],"follow-up":[116],"experimental":[117],"datasets":[118],"were":[120],"used":[121],"validation.":[123],"provide":[125],"default":[126],"pipelines,":[127],"but":[128],"combined":[133],"other":[135],"data":[136,167],"analysis":[137],"methods":[138],"help":[141],"assess":[142],"their":[143],"relative":[144],"merits.":[145],"AVAILABILITY":[146],"AND":[147],"IMPLEMENTATION:":[148],"casper":[149],"package":[150],"at":[151,158,170],"www.bioconductor.org/packages/release/bioc/html/casper.html,":[152],"Supplementary":[153,166],"Manual":[154],"by":[155],"typing":[156],"casperDesign()":[157],"R":[160],"prompt.":[161],"CONTACT:":[162],"rosselldavid@gmail.com":[163],"SUPPLEMENTARY":[164],"INFORMATION:":[165],"available":[169],"Bioinformatics":[171],"online.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2016-06-24T00:00:00"}