{"id":"https://openalex.org/W2888299778","doi":"https://doi.org/10.1093/bioinformatics/bty706","title":"checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes","display_name":"checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes","publication_year":2018,"publication_date":"2018-08-23","ids":{"openalex":"https://openalex.org/W2888299778","doi":"https://doi.org/10.1093/bioinformatics/bty706","mag":"2888299778","pmid":"https://pubmed.ncbi.nlm.nih.gov/30165585"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty706","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty706","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/901/48965813/bioinformatics_35_5_901.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/901/48965813/bioinformatics_35_5_901.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006612133","display_name":"Hugo Varet","orcid":"https://orcid.org/0000-0003-3980-4463"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210162100","display_name":"Department of Genomes & Genetics","ror":"https://ror.org/05etkex69","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I157536573","https://openalex.org/I4210096427","https://openalex.org/I4210162100"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Hugo Varet","raw_affiliation_strings":["Center for Technological Resources and Research, Institut Pasteur \u2013 Transcriptome and Epigenome Platform \u2013 Biomics Pole \u2013 C2RT, Paris, France","Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur \u2013 Bioinformatics and Biostatistics Hub \u2013 C3BI, USR 3756 IP CNRS, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Technological Resources and Research, Institut Pasteur \u2013 Transcriptome and Epigenome Platform \u2013 Biomics Pole \u2013 C2RT, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I4210162100"]},{"raw_affiliation_string":"Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur \u2013 Bioinformatics and Biostatistics Hub \u2013 C3BI, USR 3756 IP CNRS, Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010453739","display_name":"Jean\u2010Yves Copp\u00e9e","orcid":"https://orcid.org/0000-0001-7747-5731"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210162100","display_name":"Department of Genomes & Genetics","ror":"https://ror.org/05etkex69","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I157536573","https://openalex.org/I4210096427","https://openalex.org/I4210162100"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jean-Yves Copp\u00e9e","raw_affiliation_strings":["Center for Technological Resources and Research, Institut Pasteur \u2013 Transcriptome and Epigenome Platform \u2013 Biomics Pole \u2013 C2RT, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Technological Resources and Research, Institut Pasteur \u2013 Transcriptome and Epigenome Platform \u2013 Biomics Pole \u2013 C2RT, Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I4210162100"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006612133"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573","https://openalex.org/I4210162100"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.4209,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.600661,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"5","first_page":"901","last_page":"902"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3319999873638153,"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":0.3319999873638153,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.21490000188350677,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.06949999928474426,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.8019071817398071},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7712371945381165},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6880233883857727},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.6184962391853333},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5688247084617615},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5209237933158875},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.49271729588508606},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.471355140209198},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4584083557128906},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4263027012348175},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.394244909286499},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3889804184436798},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3652530312538147},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3560831546783447},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2535870671272278},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19694864749908447},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.14941740036010742},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1463877558708191},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13547569513320923},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0648786723613739}],"concepts":[{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.8019071817398071},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7712371945381165},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6880233883857727},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.6184962391853333},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5688247084617615},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5209237933158875},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.49271729588508606},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.471355140209198},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4584083557128906},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4263027012348175},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.394244909286499},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3889804184436798},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3652530312538147},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3560831546783447},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2535870671272278},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19694864749908447},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.14941740036010742},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1463877558708191},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13547569513320923},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0648786723613739},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[{"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":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty706","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty706","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/901/48965813/bioinformatics_35_5_901.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30165585","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30165585","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:HAL:pasteur-02557485v1","is_oa":true,"landing_page_url":"https://pasteur.hal.science/pasteur-02557485","pdf_url":"https://pasteur.hal.science/pasteur-02557485v1/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Bioinformatics, 2019, 35 (5), pp.901-902. ⟨10.1093/bioinformatics/bty706⟩","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:5389908","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6394397","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6394397","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6394397","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty706","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty706","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/901/48965813/bioinformatics_35_5_901.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2483067034","display_name":"Organisation et mont\u00e9e en puissance d'une Infrastructure Nationale de G\u00e9nomique","funder_award_id":"ANR-10-INBS-0009","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2888299778.pdf","grobid_xml":"https://content.openalex.org/works/W2888299778.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W2141599418","https://openalex.org/W2396849069"],"related_works":["https://openalex.org/W2380602769","https://openalex.org/W3177221076","https://openalex.org/W2365343424","https://openalex.org/W3033962221","https://openalex.org/W2377966044","https://openalex.org/W2080298153","https://openalex.org/W4236942186","https://openalex.org/W2888299778","https://openalex.org/W2415345264","https://openalex.org/W1974719404"],"abstract_inverted_index":{"SUMMARY:":[0],"When":[1],"sequencing":[2],"several":[3],"libraries":[4],"simultaneously,":[5],"the":[6,18,25,54,57,64],"selection":[7,55],"of":[8,11,56,63,74],"compatible":[9],"combinations":[10],"indexes":[12,59],"is":[13,71,87],"critical":[14],"for":[15],"ensuring":[16],"that":[17,52],"sequencer":[19],"will":[20],"be":[21],"able":[22],"to":[23,30,38],"decipher":[24],"short,":[26],"sample-specific":[27],"barcodes":[28],"added":[29],"each":[31],"fragment.":[32],"However,":[33],"researchers":[34],"have":[35],"few":[36],"tools":[37],"help":[39],"them":[40],"choose":[41],"optimal":[42],"indexes.":[43],"Here,":[44],"we":[45],"present":[46],"checkMyIndex,":[47],"an":[48,79],"online":[49],"R/Shiny":[50,82],"application":[51],"facilitates":[53],"right":[58],"as":[60,78],"a":[61],"function":[62],"experimental":[65],"constraints.":[66],"AVAILABILITY":[67],"AND":[68],"IMPLEMENTATION:":[69],"checkMyIndex":[70],"available":[72,88],"free":[73],"charge":[75],"at":[76,91],"https://checkmyindex.pasteur.fr":[77],"online,":[80],"web-based":[81],"application.":[83],"The":[84],"source":[85],"code":[86],"on":[89],"GitHub":[90],"https://github.com/PF2-pasteur-fr/checkMyIndex.":[92]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}