{"id":"https://openalex.org/W2799170276","doi":"https://doi.org/10.1186/s12859-018-2139-9","title":"VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis","display_name":"VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis","publication_year":2018,"publication_date":"2018-04-12","ids":{"openalex":"https://openalex.org/W2799170276","doi":"https://doi.org/10.1186/s12859-018-2139-9","mag":"2799170276","pmid":"https://pubmed.ncbi.nlm.nih.gov/29649993"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2139-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2139-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2139-9","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/track/pdf/10.1186/s12859-018-2139-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054124194","display_name":"MacIntosh Cornwell","orcid":"https://orcid.org/0000-0002-3041-4410"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"MacIntosh Cornwell","raw_affiliation_strings":["Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062252494","display_name":"Mahesh Vangala","orcid":null},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mahesh Vangala","raw_affiliation_strings":["University of Massachusetts Medical School, Worcester, MA, 01655, USA"],"affiliations":[{"raw_affiliation_string":"University of Massachusetts Medical School, Worcester, MA, 01655, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055277353","display_name":"Len Taing","orcid":"https://orcid.org/0000-0001-7453-5372"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Len Taing","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080768582","display_name":"Zachary T. Herbert","orcid":"https://orcid.org/0000-0001-9401-2464"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zachary Herbert","raw_affiliation_strings":["Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005124395","display_name":"Johannes K\u00f6ster","orcid":"https://orcid.org/0000-0001-9818-9320"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Johannes K\u00f6ster","raw_affiliation_strings":["Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany","institution_ids":["https://openalex.org/I62318514"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100374468","display_name":"Bo Li","orcid":"https://orcid.org/0000-0002-8617-900X"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bo Li","raw_affiliation_strings":["Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016231964","display_name":"Hanfei Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanfei Sun","raw_affiliation_strings":["Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai, 200092, China"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai, 200092, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036664787","display_name":"Taiwen Li","orcid":"https://orcid.org/0000-0001-7940-8196"},"institutions":[{"id":"https://openalex.org/I4391768043","display_name":"State Key Laboratory of Oral Diseases","ror":"https://ror.org/00pvqk557","country_code":null,"type":"facility","lineage":["https://openalex.org/I24185976","https://openalex.org/I4391768043"]},{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Taiwen Li","raw_affiliation_strings":["State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4391768043"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100723164","display_name":"Jian Zhang","orcid":"https://orcid.org/0000-0002-4966-2086"},"institutions":[{"id":"https://openalex.org/I142415962","display_name":"Beijing Institute of Education","ror":"https://ror.org/03aefdx31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I142415962"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Zhang","raw_affiliation_strings":["Beijing Institute of Basic Medical Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Beijing Institute of Basic Medical Sciences, Beijing, China","institution_ids":["https://openalex.org/I142415962","https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041427080","display_name":"Xintao Qiu","orcid":"https://orcid.org/0000-0002-8560-7017"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xintao Qiu","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012006306","display_name":"Matthew Pun","orcid":"https://orcid.org/0000-0002-4766-4301"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Pun","raw_affiliation_strings":["Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051714606","display_name":"Rinath Jeselsohn","orcid":"https://orcid.org/0000-0001-7996-7529"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rinath Jeselsohn","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033532061","display_name":"Myles Brown","orcid":"https://orcid.org/0000-0002-8213-1658"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Myles Brown","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045575546","display_name":"X. Shirley Liu","orcid":"https://orcid.org/0000-0003-4736-7339"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X. Shirley Liu","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, 02215, USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066070097","display_name":"Henry W. Long","orcid":"https://orcid.org/0000-0001-6849-6629"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Henry W. Long","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. henry_long@dfci.harvard.edu","Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. henry_long@dfci.harvard.edu","Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA"],"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. henry_long@dfci.harvard.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. henry_long@dfci.harvard.edu","institution_ids":[]},{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5054124194"],"corresponding_institution_ids":["https://openalex.org/I4210117453"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":9.4021,"has_fulltext":true,"cited_by_count":227,"citation_normalized_percentile":{"value":0.98714204,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"19","issue":"1","first_page":"135","last_page":"135"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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":0.9980000257492065,"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":0.9976999759674072,"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":0.996399998664856,"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/workflow","display_name":"Workflow","score":0.6945244669914246},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6452142000198364},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6203520894050598},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4698913097381592},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4342024028301239},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3737349808216095},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3287245035171509},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32168805599212646},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.2021140456199646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16899579763412476},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09286037087440491},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08597606420516968}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6945244669914246},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6452142000198364},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6203520894050598},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4698913097381592},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4342024028301239},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3737349808216095},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3287245035171509},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32168805599212646},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2021140456199646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16899579763412476},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09286037087440491},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08597606420516968},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"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":"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":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015536","descriptor_name":"Down-Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015536","descriptor_name":"Down-Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015536","descriptor_name":"Down-Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015854","descriptor_name":"Up-Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015854","descriptor_name":"Up-Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015854","descriptor_name":"Up-Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-018-2139-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2139-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2139-9","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:29649993","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29649993","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":null},{"id":"pmh:oai:escholarship.umassmed.edu:oapubs-4464","is_oa":true,"landing_page_url":"https://escholarship.umassmed.edu/oapubs/3453","pdf_url":"https://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=4464&context=oapubs","source":{"id":"https://openalex.org/S4306400883","display_name":"The Journal of the American Medical Association (JAMA) Network (American Medical Association)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173654999","host_organization_name":"American Medical Association","host_organization_lineage":["https://openalex.org/I173654999"],"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":"Open Access Publications by UMMS Authors","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:05f5ce1145074e0bbe0ea6794782fc82","is_oa":true,"landing_page_url":"https://doaj.org/article/05f5ce1145074e0bbe0ea6794782fc82","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-14 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4835000","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5897949","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5897949","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5897949","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2139-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2139-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2139-9","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":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G1592916131","display_name":null,"funder_award_id":"31329003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5003582939","display_name":null,"funder_award_id":"CA180980","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7635463304","display_name":null,"funder_award_id":"U01 CA180980","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2799170276.pdf","grobid_xml":"https://content.openalex.org/works/W2799170276.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1836811906","https://openalex.org/W1981509058","https://openalex.org/W2035322315","https://openalex.org/W2035618305","https://openalex.org/W2060842569","https://openalex.org/W2060880575","https://openalex.org/W2064469303","https://openalex.org/W2070494252","https://openalex.org/W2074414424","https://openalex.org/W2091303550","https://openalex.org/W2096000928","https://openalex.org/W2096192437","https://openalex.org/W2106578986","https://openalex.org/W2110417468","https://openalex.org/W2116528446","https://openalex.org/W2122855404","https://openalex.org/W2127081697","https://openalex.org/W2136430672","https://openalex.org/W2137586531","https://openalex.org/W2138255346","https://openalex.org/W2139399606","https://openalex.org/W2140600399","https://openalex.org/W2141224543","https://openalex.org/W2141458291","https://openalex.org/W2146512944","https://openalex.org/W2148802388","https://openalex.org/W2155943701","https://openalex.org/W2156066129","https://openalex.org/W2158274053","https://openalex.org/W2169353806","https://openalex.org/W2169456326","https://openalex.org/W2179438025","https://openalex.org/W2191643803","https://openalex.org/W2222859485","https://openalex.org/W2228647225","https://openalex.org/W2236822143","https://openalex.org/W2334045973","https://openalex.org/W2406250479","https://openalex.org/W2411861063","https://openalex.org/W2416083568","https://openalex.org/W2507880739","https://openalex.org/W2577896867","https://openalex.org/W2603756957","https://openalex.org/W2607938959","https://openalex.org/W6704052225"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W188202134","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2068608913"],"abstract_inverted_index":{"VIPER":[0],"is":[1],"a":[2,15],"comprehensive":[3],"solution":[4],"that":[5],"performs":[6],"most":[7],"standard":[8],"RNA-seq":[9],"analyses":[10],"quickly":[11],"and":[12,20],"effectively":[13],"with":[14],"built-in":[16],"capacity":[17],"for":[18],"customization":[19],"expansion.":[21]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":28},{"year":2023,"cited_by_count":35},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":42},{"year":2020,"cited_by_count":33},{"year":2019,"cited_by_count":22},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}