{"id":"https://openalex.org/W3012529551","doi":"https://doi.org/10.1186/s12859-020-3433-x","title":"RASflow: an RNA-Seq analysis workflow with Snakemake","display_name":"RASflow: an RNA-Seq analysis workflow with Snakemake","publication_year":2020,"publication_date":"2020-03-17","ids":{"openalex":"https://openalex.org/W3012529551","doi":"https://doi.org/10.1186/s12859-020-3433-x","mag":"3012529551","pmid":"https://pubmed.ncbi.nlm.nih.gov/32183729"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-3433-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3433-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3433-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3433-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100412327","display_name":"Xiaokang Zhang","orcid":"https://orcid.org/0000-0003-4684-317X"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Xiaokang Zhang","raw_affiliation_strings":["Computational Biology Unit, Department of Informatics, University of Bergen, Thormohlens Gate 55, Bergen, 5009, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Unit, Department of Informatics, University of Bergen, Thormohlens Gate 55, Bergen, 5009, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012964587","display_name":"Inge Jonassen","orcid":"https://orcid.org/0000-0003-4110-0748"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Inge Jonassen","raw_affiliation_strings":["Computational Biology Unit, Department of Informatics, University of Bergen, Thormohlens Gate 55, Bergen, 5009, Norway. inge.jonassen@uib.no","Computational Biology Unit, Department of Informatics, University of Bergen, Thormohlens Gate 55, Bergen, 5009, Norway"],"raw_orcid":"https://orcid.org/0000-0003-4110-0748","affiliations":[{"raw_affiliation_string":"Computational Biology Unit, Department of Informatics, University of Bergen, Thormohlens Gate 55, Bergen, 5009, Norway. inge.jonassen@uib.no","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Computational Biology Unit, Department of Informatics, University of Bergen, Thormohlens Gate 55, Bergen, 5009, Norway","institution_ids":["https://openalex.org/I4432739"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012964587"],"corresponding_institution_ids":["https://openalex.org/I4432739"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.9821,"has_fulltext":true,"cited_by_count":72,"citation_normalized_percentile":{"value":0.92505116,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"21","issue":"1","first_page":"110","last_page":"110"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7904000282287598,"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":0.7904000282287598,"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":0.09440000355243683,"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/T10885","display_name":"Gene expression and cancer classification","score":0.016100000590085983,"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":0.9210447072982788},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7133479118347168},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5926297307014465},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.5258208513259888},{"id":"https://openalex.org/keywords/usable","display_name":"USable","score":0.5155913233757019},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.48558467626571655},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47871851921081543},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.42899060249328613},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4133242964744568},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4065510928630829},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.366128146648407},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.354162335395813},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3469407260417938},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.3055720627307892},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.24791273474693298},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1502198576927185},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1380552351474762},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13682019710540771},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1322295367717743},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09226414561271667}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.9210447072982788},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7133479118347168},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5926297307014465},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.5258208513259888},{"id":"https://openalex.org/C2780615836","wikidata":"https://www.wikidata.org/wiki/Q2471869","display_name":"USable","level":2,"score":0.5155913233757019},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.48558467626571655},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47871851921081543},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.42899060249328613},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4133242964744568},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4065510928630829},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.366128146648407},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.354162335395813},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3469407260417938},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3055720627307892},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.24791273474693298},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1502198576927185},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1380552351474762},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13682019710540771},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1322295367717743},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09226414561271667}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","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":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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D057188","descriptor_name":"Workflow","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":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-020-3433-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3433-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3433-x","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:32183729","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32183729","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:doaj.org/article:ff7ff3d95cb4415c92736a8606773366","is_oa":true,"landing_page_url":"https://doaj.org/article/ff7ff3d95cb4415c92736a8606773366","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"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 21, Iss 1, Pp 1-9 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7079470","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7079470","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/s12859-020-3433-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3433-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3433-x","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":[{"display_name":"Quality Education","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G4160626084","display_name":null,"funder_award_id":"248840","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"}],"funders":[{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3012529551.pdf","grobid_xml":"https://content.openalex.org/works/W3012529551.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1972924519","https://openalex.org/W2046233258","https://openalex.org/W2065128082","https://openalex.org/W2067151470","https://openalex.org/W2097186235","https://openalex.org/W2099879295","https://openalex.org/W2100596675","https://openalex.org/W2102278945","https://openalex.org/W2105067980","https://openalex.org/W2106319366","https://openalex.org/W2107018762","https://openalex.org/W2110417468","https://openalex.org/W2111281047","https://openalex.org/W2114104545","https://openalex.org/W2116041602","https://openalex.org/W2118258530","https://openalex.org/W2119185338","https://openalex.org/W2130116522","https://openalex.org/W2134526812","https://openalex.org/W2138207763","https://openalex.org/W2152239989","https://openalex.org/W2169456326","https://openalex.org/W2179438025","https://openalex.org/W2197124664","https://openalex.org/W2323326409","https://openalex.org/W2432815617","https://openalex.org/W2571745526","https://openalex.org/W2577896867","https://openalex.org/W2592811885","https://openalex.org/W2731748842","https://openalex.org/W2799170276","https://openalex.org/W2806313121","https://openalex.org/W2898321887","https://openalex.org/W2921922051","https://openalex.org/W2939484987","https://openalex.org/W2949095907","https://openalex.org/W2949583997","https://openalex.org/W2963367647","https://openalex.org/W2976294948","https://openalex.org/W4237403594"],"related_works":["https://openalex.org/W2375304607","https://openalex.org/W2391168633","https://openalex.org/W2353477037","https://openalex.org/W2385499106","https://openalex.org/W2110462752","https://openalex.org/W1574425962","https://openalex.org/W4310820052","https://openalex.org/W2354357087","https://openalex.org/W2352774566","https://openalex.org/W4243836028"],"abstract_inverted_index":{"BACKGROUND:":[0],"With":[1],"the":[2,30,54,92,123,139,151,157,205],"cost":[3],"of":[4,10,27,40,46,48,53,59,80,91,100,116,201,207,220,252],"DNA":[5],"sequencing":[6],"decreasing,":[7],"increasing":[8],"amounts":[9],"RNA-Seq":[11,31,170,173,266],"data":[12,32,76,85,87,117],"are":[13,61,95],"being":[14],"generated":[15],"giving":[16],"novel":[17,81],"insight":[18],"into":[19],"gene":[20,28],"expression":[21,47],"and":[22,118,121,131,156,168,180,187,190,212,233,264],"regulation.":[23],"Prior":[24],"to":[25,34,63,77,97,105,112,137,209],"analysis":[26,119,171,267],"expression,":[29],"has":[33,216],"be":[35,195,225,242],"processed":[36],"through":[37],"a":[38,44,107,113,165,198,217,262],"number":[39,58],"steps":[41,68],"resulting":[42],"in":[43,51,86,230],"quantification":[45],"each":[49,52],"gene/transcript":[50],"analyzed":[55],"samples.":[56],"A":[57],"workflows":[60,94],"available":[62,255],"help":[64],"researchers":[65,228,245],"perform":[66],"these":[67],"on":[69,74,128,256],"their":[70],"own":[71],"data,":[72],"or":[73,83],"public":[75],"take":[78],"advantage":[79],"software":[82],"reference":[84],"re-analysis.":[88],"However,":[89],"many":[90,270],"existing":[93],"limited":[96,146],"specific":[98],"types":[99],"studies.":[101],"We":[102],"therefore":[103],"aimed":[104,136],"develop":[106],"maximally":[108],"general":[109],"workflow,":[110],"applicable":[111,196],"wide":[114,199],"range":[115,219],"approaches":[120],"at":[122],"same":[124],"time":[125],"support":[126],"research":[127],"both":[129,210],"model":[130],"non-model":[132],"organisms.":[133],"Furthermore,":[134],"we":[135,162],"make":[138],"workflow":[140,152,268],"usable":[141],"also":[142,191],"for":[143,197],"users":[144],"with":[145,184,246],"programming":[147,238],"skills.":[148],"RESULTS:":[149],"Utilizing":[150,178],"management":[153,159],"system":[154,160],"Snakemake":[155,175,179],"package":[158],"Conda,":[161],"have":[163],"developed":[164],"modular,":[166],"flexible":[167],"user-friendly":[169],"workflow:":[172],"Analysis":[174],"Workflow":[176],"(RASflow).":[177],"Conda":[181],"alleviates":[182],"challenges":[183],"library":[185],"dependencies":[186],"version":[188],"conflicts":[189],"supports":[192,204],"reproducibility.":[193],"To":[194],"variety":[200],"applications,":[202],"RASflow":[203,215,253,260],"mapping":[206],"reads":[208],"genomic":[211],"transcriptomic":[213],"assemblies.":[214],"broad":[218],"potential":[221],"users:":[222],"it":[223,235,240],"can":[224,241],"applied":[226],"by":[227,244],"interested":[229],"any":[231],"organism":[232],"since":[234],"requires":[236],"no":[237],"skills,":[239],"used":[243],"different":[247],"backgrounds.":[248],"The":[249],"source":[250],"code":[251],"is":[254,261],"GitHub:":[257],"https://github.com/zhxiaokang/RASflow.":[258],"CONCLUSIONS:":[259],"simple":[263],"reliable":[265],"covering":[269],"use":[271],"cases.":[272]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
