{"id":"https://openalex.org/W2903897193","doi":"https://doi.org/10.7287/peerj.preprints.27317v2","title":"A comprehensive RNA-Seq pipeline includes meta-analysis, interactivity and automatic reporting","display_name":"A comprehensive RNA-Seq pipeline includes meta-analysis, interactivity and automatic reporting","publication_year":2018,"publication_date":"2018-11-05","ids":{"openalex":"https://openalex.org/W2903897193","doi":"https://doi.org/10.7287/peerj.preprints.27317v2","mag":"2903897193"},"language":"en","primary_location":{"id":"doi:10.7287/peerj.preprints.27317v2","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27317v2","pdf_url":"https://peerj.com/preprints/27317.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://peerj.com/preprints/27317.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033693548","display_name":"Giulio Spinozzi","orcid":"https://orcid.org/0000-0002-4220-2474"},"institutions":[{"id":"https://openalex.org/I27483092","display_name":"University of Perugia","ror":"https://ror.org/00x27da85","country_code":"IT","type":"education","lineage":["https://openalex.org/I27483092"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Giulio Spinozzi","raw_affiliation_strings":["Department of Medicine, University of Perugia, Perugia, Italy"],"raw_orcid":"https://orcid.org/0000-0002-4220-2474","affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Perugia, Perugia, Italy","institution_ids":["https://openalex.org/I27483092"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086219170","display_name":"Valentina Tini","orcid":null},"institutions":[{"id":"https://openalex.org/I27483092","display_name":"University of Perugia","ror":"https://ror.org/00x27da85","country_code":"IT","type":"education","lineage":["https://openalex.org/I27483092"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Valentina Tini","raw_affiliation_strings":["Department of Medicine, University of Perugia, Perugia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Perugia, Perugia, Italy","institution_ids":["https://openalex.org/I27483092"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088269711","display_name":"Laura Mincarelli","orcid":"https://orcid.org/0000-0002-9222-2676"},"institutions":[{"id":"https://openalex.org/I27483092","display_name":"University of Perugia","ror":"https://ror.org/00x27da85","country_code":"IT","type":"education","lineage":["https://openalex.org/I27483092"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Laura Mincarelli","raw_affiliation_strings":["Department of Medicine, University of Perugia, Perugia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Perugia, Perugia, Italy","institution_ids":["https://openalex.org/I27483092"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008077055","display_name":"Brunangelo Falini","orcid":"https://orcid.org/0000-0002-7198-5965"},"institutions":[{"id":"https://openalex.org/I27483092","display_name":"University of Perugia","ror":"https://ror.org/00x27da85","country_code":"IT","type":"education","lineage":["https://openalex.org/I27483092"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Brunangelo Falini","raw_affiliation_strings":["Department of Medicine, University of Perugia, Perugia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Perugia, Perugia, Italy","institution_ids":["https://openalex.org/I27483092"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089614080","display_name":"Maria Paola Martelli","orcid":"https://orcid.org/0000-0001-9139-1729"},"institutions":[{"id":"https://openalex.org/I27483092","display_name":"University of Perugia","ror":"https://ror.org/00x27da85","country_code":"IT","type":"education","lineage":["https://openalex.org/I27483092"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Maria Paola Martelli","raw_affiliation_strings":["Department of Medicine, University of Perugia, Perugia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Perugia, Perugia, Italy","institution_ids":["https://openalex.org/I27483092"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5033693548"],"corresponding_institution_ids":["https://openalex.org/I27483092"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.11819049,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"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":0.991100013256073,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9846000075340271,"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/pipeline","display_name":"Pipeline (software)","score":0.8856793642044067},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7321740984916687},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.7170174717903137},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.63026362657547},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47630274295806885},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4711189270019531},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4158870577812195},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.25080615282058716},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22617363929748535},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17819544672966003},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14700722694396973},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1183464527130127},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09357896447181702},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08764529228210449}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8856793642044067},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7321740984916687},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7170174717903137},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.63026362657547},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47630274295806885},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4711189270019531},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4158870577812195},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.25080615282058716},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22617363929748535},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17819544672966003},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14700722694396973},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1183464527130127},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09357896447181702},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08764529228210449},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.7287/peerj.preprints.27317v2","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27317v2","pdf_url":"https://peerj.com/preprints/27317.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.7287/peerj.preprints.27317v2","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27317v2","pdf_url":"https://peerj.com/preprints/27317.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2903897193.pdf","grobid_xml":"https://content.openalex.org/works/W2903897193.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1787170397","https://openalex.org/W4292347844","https://openalex.org/W2897593847"],"abstract_inverted_index":{"There":[0],"are":[1],"many":[2],"methods":[3],"available":[4],"for":[5,128,131,135],"each":[6,13,83,102],"phase":[7],"of":[8,14,34,61,89,114,126],"the":[9,29,49,74,77,87,96,107,124,149,163],"RNA-Seq":[10,54,57],"analysis":[11,80],"and":[12,36,91,93,116,133,174,187],"them":[15],"uses":[16],"different":[17,44,62,159],"algorithms.":[18],"It":[19,104],"is":[20,120],"therefore":[21],"useful":[22],"to":[23,76,148,156],"identify":[24],"a":[25,166,171,190],"pipeline":[26,108,143,164],"that":[27,106,121,144,169],"combines":[28],"best":[30],"tools":[31,52],"in":[32,53,182,189],"terms":[33],"time":[35,92],"results.":[37],"For":[38,82],"this":[39],"purpose,":[40],"we":[41,69,85,139],"compared":[42,70,95],"five":[43,71],"pipelines,":[45],"obtained":[46],"by":[47,101,146],"combining":[48],"most":[50],"used":[51],"analysis.":[55,137,176],"Using":[56],"data":[58],"on":[59],"samples":[60],"Acute":[63],"Myeloid":[64],"Leukemia":[65],"(AML)":[66],"cell":[67],"lines,":[68],"pipelines":[72],"from":[73],"alignment":[75],"differential":[78,136],"expression":[79],"(DEA).":[81],"one":[84],"evaluated":[86],"peak":[88],"RAM":[90,115],"then":[94],"differentially":[97],"expressed":[98],"genes":[99],"identified":[100],"pipeline.":[103],"emerged":[105],"with":[109],"shorter":[110],"times,":[111],"lower":[112],"consumption":[113],"more":[117],"reliable":[118],"results,":[119],"which":[122],"involves":[123],"use":[125],"HISAT2":[127],"alignment,":[129],"featureCounts":[130],"quantification":[132],"edgeR":[134],"Finally,":[138],"developed":[140],"an":[141,183],"automated":[142],"recurs":[145],"default":[147],"cited":[150],"pipeline,":[151],"but":[152],"it":[153],"also":[154],"allows":[155],"choose":[157],"between":[158],"tools.":[160],"In":[161],"addition,":[162],"makes":[165],"final":[167],"meta-analysis":[168],"includes":[170],"Gene":[172],"Ontology":[173],"Pathway":[175],"The":[177],"results":[178],"can":[179],"be":[180],"viewed":[181],"interactive":[184],"Shiny":[185],"App":[186],"exported":[188],"report":[191],"(pdf,":[192],"word":[193],"or":[194],"html":[195],"formats).":[196]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-25T14:43:58.451035","created_date":"2025-10-10T00:00:00"}