{"id":"https://openalex.org/W2105479306","doi":"https://doi.org/10.1093/bioinformatics/btr700","title":"<tt>htSeqTools</tt>: high-throughput sequencing quality control, processing and visualization in R","display_name":"<tt>htSeqTools</tt>: high-throughput sequencing quality control, processing and visualization in R","publication_year":2011,"publication_date":"2011-12-22","ids":{"openalex":"https://openalex.org/W2105479306","doi":"https://doi.org/10.1093/bioinformatics/btr700","mag":"2105479306","pmid":"https://pubmed.ncbi.nlm.nih.gov/22199381"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/589/48878713/bioinformatics_28_4_589.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/589/48878713/bioinformatics_28_4_589.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002962251","display_name":"Evarist Planet","orcid":"https://orcid.org/0000-0002-5464-5379"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Evarist Planet","raw_affiliation_strings":["1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085139761","display_name":"Camille Stephan\u2010Otto Attolini","orcid":"https://orcid.org/0000-0001-8045-320X"},"institutions":[{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Camille Stephan-Otto Attolini","raw_affiliation_strings":["1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017431278","display_name":"\u00d3scar Reina","orcid":"https://orcid.org/0000-0002-1031-2732"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Oscar Reina","raw_affiliation_strings":["1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045437819","display_name":"Oscar Flores","orcid":null},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Oscar Flores","raw_affiliation_strings":["1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063900043","display_name":"David Rossell","orcid":"https://orcid.org/0000-0002-7104-5789"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"David Rossell","raw_affiliation_strings":["1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"1 Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine of Barcelona, Barcelona and 2IRB-BSC Joint Research Program on Computational Biology, IRB Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002962251"],"corresponding_institution_ids":["https://openalex.org/I4210122345","https://openalex.org/I9617848"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8676,"has_fulltext":true,"cited_by_count":65,"citation_normalized_percentile":{"value":0.8544446,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"28","issue":"4","first_page":"589","last_page":"590"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","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/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"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.9868404865264893},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.8117028474807739},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6769945621490479},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.6163783073425293},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5205836892127991},{"id":"https://openalex.org/keywords/outlier","display_name":"Outlier","score":0.47876110672950745},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42763713002204895},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4118501543998718},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37362226843833923},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2605632543563843},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13370764255523682},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12055948376655579},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08979874849319458},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07555407285690308},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.06600457429885864}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9868404865264893},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.8117028474807739},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6769945621490479},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.6163783073425293},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5205836892127991},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.47876110672950745},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42763713002204895},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4118501543998718},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37362226843833923},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2605632543563843},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13370764255523682},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12055948376655579},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08979874849319458},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07555407285690308},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.06600457429885864},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":"D020407","descriptor_name":"Internet","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":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btr700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/589/48878713/bioinformatics_28_4_589.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22199381","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22199381","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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/589/48878713/bioinformatics_28_4_589.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4822440573","display_name":null,"funder_award_id":"RETICS","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G7462530143","display_name":null,"funder_award_id":"RETIC","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"}],"funders":[{"id":"https://openalex.org/F4320309991","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2105479306.pdf","grobid_xml":"https://content.openalex.org/works/W2105479306.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2074089196","https://openalex.org/W2160697532","https://openalex.org/W2168175751","https://openalex.org/W2171808845","https://openalex.org/W2801655566","https://openalex.org/W3013289126"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W2128360321","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2133055377","https://openalex.org/W2921090651"],"abstract_inverted_index":{"www.bioconductor.org.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
