{"id":"https://openalex.org/W2577896867","doi":"https://doi.org/10.1093/bib/bbw143","title":"hppRNA\u2014a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples","display_name":"hppRNA\u2014a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples","publication_year":2016,"publication_date":"2016-12-14","ids":{"openalex":"https://openalex.org/W2577896867","doi":"https://doi.org/10.1093/bib/bbw143","mag":"2577896867","pmid":"https://pubmed.ncbi.nlm.nih.gov/28096075"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbw143","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbw143","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100416781","display_name":"Dapeng Wang","orcid":"https://orcid.org/0000-0002-9925-4574"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Dapeng Wang","raw_affiliation_strings":["Department of Plant Sciences, University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Department of Plant Sciences, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100416781"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.0917,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.87645355,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"19","issue":"4","first_page":"bbw143","last_page":"bbw143"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9986000061035156,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/perl","display_name":"Perl","score":0.7551462650299072},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7132272124290466},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.672956645488739},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6664738655090332},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6559743881225586},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4913310110569},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.46661725640296936},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4593442380428314},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37503811717033386},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3026086091995239},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.2851864695549011},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2583566904067993},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19791001081466675},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18236622214317322},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.17257905006408691},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1692942976951599}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.7551462650299072},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7132272124290466},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.672956645488739},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6664738655090332},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6559743881225586},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4913310110569},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.46661725640296936},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4593442380428314},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37503811717033386},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3026086091995239},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2851864695549011},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2583566904067993},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19791001081466675},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18236622214317322},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.17257905006408691},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1692942976951599},{"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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"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":"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbw143","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbw143","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28096075","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28096075","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4399999976158142,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1544792501","https://openalex.org/W1575937113","https://openalex.org/W1964916549","https://openalex.org/W1981509058","https://openalex.org/W1983275320","https://openalex.org/W1990293955","https://openalex.org/W1999574084","https://openalex.org/W2036897871","https://openalex.org/W2036913140","https://openalex.org/W2040909468","https://openalex.org/W2053782598","https://openalex.org/W2060842569","https://openalex.org/W2095932050","https://openalex.org/W2096465161","https://openalex.org/W2102014391","https://openalex.org/W2102278945","https://openalex.org/W2104005232","https://openalex.org/W2108234281","https://openalex.org/W2109288169","https://openalex.org/W2110417468","https://openalex.org/W2110905563","https://openalex.org/W2114104545","https://openalex.org/W2117677974","https://openalex.org/W2119180969","https://openalex.org/W2119298573","https://openalex.org/W2120500419","https://openalex.org/W2121180999","https://openalex.org/W2124097252","https://openalex.org/W2131136499","https://openalex.org/W2133233871","https://openalex.org/W2136482257","https://openalex.org/W2138093837","https://openalex.org/W2138207763","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2141544545","https://openalex.org/W2143051000","https://openalex.org/W2146728635","https://openalex.org/W2147761046","https://openalex.org/W2159479647","https://openalex.org/W2162816478","https://openalex.org/W2166820820","https://openalex.org/W2167321137","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2172194140","https://openalex.org/W2174938954","https://openalex.org/W2176686025","https://openalex.org/W2179438025","https://openalex.org/W2196247406","https://openalex.org/W2228647225","https://openalex.org/W2236822143","https://openalex.org/W2254034232","https://openalex.org/W2323326409","https://openalex.org/W2620721366","https://openalex.org/W2949081006","https://openalex.org/W2951957292","https://openalex.org/W4243836338"],"related_works":["https://openalex.org/W2331989206","https://openalex.org/W3173828731","https://openalex.org/W45658120","https://openalex.org/W2008612003","https://openalex.org/W4205178530","https://openalex.org/W613088223","https://openalex.org/W2739025131","https://openalex.org/W2606876474","https://openalex.org/W1974405519","https://openalex.org/W4287121746"],"abstract_inverted_index":{"RNA-Seq":[0],"technology":[1,112],"has":[2,28],"been":[3,29],"gradually":[4],"becoming":[5],"a":[6,25,50,60,80,134,193],"routine":[7],"approach":[8],"for":[9,39,187,202],"characterizing":[10],"the":[11,32,46,56,110,147,164,189,203,209,220],"properties":[12],"of":[13,17,34,53,66,82,95,115,142,166,196],"transcriptome":[14],"in":[15,130,198],"terms":[16],"organisms,":[18],"cell":[19],"types":[20],"and":[21,23,74,85,91,127,155,175],"conditions":[22],"consequently":[24],"big":[26],"burden":[27],"put":[30],"on":[31,89,192,211],"facet":[33],"data":[35],"analysis,":[36],"which":[37,132],"calls":[38],"an":[40],"easy-to-learn":[41],"workflow":[42],"to":[43,207],"cope":[44],"with":[45,113],"increased":[47],"demands":[48],"from":[49],"large":[51],"number":[52],"laboratories":[54],"across":[55],"world.":[57],"We":[58],"report":[59],"one-in-all":[61],"solution":[62],"called":[63],"hppRNA,":[64],"composed":[65],"four":[67],"scenarios":[68],"such":[69,119],"as":[70,120,161,163,217,219],"pre-mapping,":[71],"core-workflow,":[72],"post-mapping":[73],"sequence":[75],"variation":[76],"detection,":[77],"written":[78],"by":[79],"series":[81],"individual":[83],"Perl":[84],"R":[86],"scripts,":[87],"counting":[88],"well-established":[90],"preinstalled":[92],"software,":[93],"irrespective":[94],"single-end":[96],"or":[97,100,159],"paired-end,":[98],"unstranded":[99],"stranded":[101],"sequencing":[102],"method.":[103],"It":[104],"features":[105],"six":[106],"independent":[107],"core-workflows":[108],"comprising":[109],"state-of-the-art":[111],"dozens":[114],"popular":[116],"cutting-edge":[117],"tools":[118],"Tophat-Cufflink-Cuffdiff,":[121],"Subread-featureCounts-DESeq2,":[122],"STAR-RSEM-EBSeq,":[123],"Bowtie-eXpress-edgeR,":[124],"kallisto-sleuth,":[125],"HISAT-StringTie-Ballgown,":[126],"embeds":[128],"itself":[129],"Snakemake,":[131],"is":[133,145,184],"modern":[135],"pipeline":[136,144,183,210],"management":[137],"system.":[138],"The":[139,215],"core":[140],"function":[141],"this":[143,182],"turning":[146],"raw":[148],"fastq":[149],"files":[150],"into":[151],"gene/isoform":[152],"expression":[153],"matrix":[154],"differentially":[156],"expressed":[157],"genes":[158],"isoforms":[160],"well":[162,218],"identification":[165],"fusion":[167],"genes,":[168],"single":[169],"nucleotide":[170],"polymorphisms,":[171],"long":[172],"noncoding":[173],"RNAs":[174],"circular":[176],"RNAs.":[177],"Last":[178],"but":[179],"not":[180],"least,":[181],"specifically":[185],"designed":[186],"performing":[188],"systematic":[190],"analysis":[191],"huge":[194],"set":[195],"samples":[197],"one":[199],"go,":[200],"ideally":[201],"researchers":[204],"who":[205],"intend":[206],"deploy":[208],"their":[212],"local":[213],"servers.":[214],"scripts":[216],"user":[221],"manual":[222],"are":[223],"freely":[224],"available":[225],"at":[226],"https://sourceforge.net/projects/hpprna/.":[227]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}