{"id":"https://openalex.org/W4387295331","doi":"https://doi.org/10.5281/zenodo.8399140","title":"Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells","display_name":"Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells","publication_year":2024,"publication_date":"2024-10-28","ids":{"openalex":"https://openalex.org/W4387295331","doi":"https://doi.org/10.5281/zenodo.8399140"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:8399141","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/8399141","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/8399141","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005542278","display_name":"Rodrigo Arcoverde Cerveira","orcid":"https://orcid.org/0000-0002-1145-2534","observed_orcids":["https://orcid.org/0000-0002-1145-2534"]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Arcoverde Cerveira, Rodrigo","raw_affiliation_strings":["Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","Center for Molecular Medicine (CMM), Sweden","Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-1145-2534","affiliations":[{"raw_affiliation_string":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","institution_ids":["https://openalex.org/I1335113835"]},{"raw_affiliation_string":"Center for Molecular Medicine (CMM), Sweden","institution_ids":[]},{"raw_affiliation_string":"Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074384812","display_name":"Klara Lenart","orcid":"https://orcid.org/0000-0002-4984-2618","observed_orcids":["https://orcid.org/0000-0002-4984-2618"]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Lenart, Klara","raw_affiliation_strings":["Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","Center for Molecular Medicine (CMM), Sweden","Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","institution_ids":["https://openalex.org/I1335113835"]},{"raw_affiliation_string":"Center for Molecular Medicine (CMM), Sweden","institution_ids":[]},{"raw_affiliation_string":"Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088798234","display_name":"Marcel Martin","orcid":"https://orcid.org/0000-0002-0680-200X","observed_orcids":["https://orcid.org/0000-0002-0680-200X"]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4387154792","display_name":"National Bioinformatics Infrastructure Sweden","ror":"https://ror.org/00enajs79","country_code":"SE","type":"other","lineage":["https://openalex.org/I123387679","https://openalex.org/I4387153960","https://openalex.org/I4387154792"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Martin, Marcel","raw_affiliation_strings":["National Bioinformatics Infrastructure Sweden (NBIS), Sweden","Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Bioinformatics Infrastructure Sweden (NBIS), Sweden","institution_ids":["https://openalex.org/I4387154792"]},{"raw_affiliation_string":"Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hinchcliff, Matthew James","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I4387154792","display_name":"National Bioinformatics Infrastructure Sweden","ror":"https://ror.org/00enajs79","country_code":"SE","type":"other","lineage":["https://openalex.org/I123387679","https://openalex.org/I4387153960","https://openalex.org/I4387154792"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Hinchcliff, Matthew James","raw_affiliation_strings":["Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","Center for Molecular Medicine (CMM), Sweden","National Bioinformatics Infrastructure Sweden (NBIS), Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","institution_ids":["https://openalex.org/I1335113835"]},{"raw_affiliation_string":"Center for Molecular Medicine (CMM), Sweden","institution_ids":[]},{"raw_affiliation_string":"National Bioinformatics Infrastructure Sweden (NBIS), Sweden","institution_ids":["https://openalex.org/I4387154792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033560948","display_name":"Fredrika Hellgren","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4387154792","display_name":"National Bioinformatics Infrastructure Sweden","ror":"https://ror.org/00enajs79","country_code":"SE","type":"other","lineage":["https://openalex.org/I123387679","https://openalex.org/I4387153960","https://openalex.org/I4387154792"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Hellgren, Fredrika","raw_affiliation_strings":["Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden","National Bioinformatics Infrastructure Sweden (NBIS), Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]},{"raw_affiliation_string":"National Bioinformatics Infrastructure Sweden (NBIS), Sweden","institution_ids":["https://openalex.org/I4387154792"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yu, Kewei","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Yu, Kewei","raw_affiliation_strings":["Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Assis Geraldo, Juliana","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4387154792","display_name":"National Bioinformatics Infrastructure Sweden","ror":"https://ror.org/00enajs79","country_code":"SE","type":"other","lineage":["https://openalex.org/I123387679","https://openalex.org/I4387153960","https://openalex.org/I4387154792"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Assis Geraldo, Juliana","raw_affiliation_strings":["National Bioinformatics Infrastructure Sweden (NBIS), Sweden","Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Bioinformatics Infrastructure Sweden (NBIS), Sweden","institution_ids":["https://openalex.org/I4387154792"]},{"raw_affiliation_string":"Division of Immunology & Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Kreslavsky, Taras","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Kreslavsky, Taras","raw_affiliation_strings":["Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","Center for Molecular Medicine (CMM), Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","institution_ids":["https://openalex.org/I1335113835"]},{"raw_affiliation_string":"Center for Molecular Medicine (CMM), Sweden","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024935433","display_name":"Sebastian Ols","orcid":"https://orcid.org/0000-0001-9784-7176","observed_orcids":["https://orcid.org/0000-0001-9784-7176"]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Ols, Sebastian","raw_affiliation_strings":["Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","Center for Molecular Medicine (CMM), Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","institution_ids":["https://openalex.org/I1335113835"]},{"raw_affiliation_string":"Center for Molecular Medicine (CMM), Sweden","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060575051","display_name":"Karin Lor\u00e9","orcid":"https://orcid.org/0000-0001-7679-9494","observed_orcids":["https://orcid.org/0000-0001-7679-9494"]},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Lor\u00e9, Karin","raw_affiliation_strings":["Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","Center for Molecular Medicine (CMM), Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Universitet and Karolinska University Hospital, Sweden","institution_ids":["https://openalex.org/I1335113835"]},{"raw_affiliation_string":"Center for Molecular Medicine (CMM), Sweden","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00057378,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8173999786376953,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8173999786376953,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.04520000144839287,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.026100000366568565,"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/single-cell-sequencing","display_name":"single-cell sequencing","score":0.5899999737739563},{"id":"https://openalex.org/keywords/flow-cytometry","display_name":"flow cytometry","score":0.9120000004768372},{"id":"https://openalex.org/keywords/single-cell-data-integration","display_name":"single-cell data integration","score":0.6620000004768372},{"id":"https://openalex.org/keywords/quality-control","display_name":"quality control","score":0.6620000004768372},{"id":"https://openalex.org/keywords/r-bioconductor-package","display_name":"R/Bioconductor package","score":0.781000018119812}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9240840673446655},{"id":"https://openalex.org/C553184892","wikidata":"https://www.wikidata.org/wiki/Q1141429","display_name":"Flow cytometry","level":2,"score":0.7105312347412109},{"id":"https://openalex.org/C76818968","wikidata":"https://www.wikidata.org/wiki/Q181940","display_name":"Sanger sequencing","level":4,"score":0.5705867409706116},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4615571200847626},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4253900647163391},{"id":"https://openalex.org/C38349280","wikidata":"https://www.wikidata.org/wiki/Q1434290","display_name":"Flow (mathematics)","level":2,"score":0.42170530557632446},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37781235575675964},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.24512329697608948},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.18996810913085938},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17625391483306885},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16188281774520874},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.07127884030342102},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06692945957183838},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:zenodo.org:8399141","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/8399141","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.5281/zenodo.8399140","doi":"https://doi.org/10.5281/zenodo.8399140","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.8399140","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.8399141","doi":"https://doi.org/10.5281/zenodo.8399141","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.8399141","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:8399141","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/8399141","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2951158909","https://openalex.org/W2910366648","https://openalex.org/W2885307522","https://openalex.org/W4413910425","https://openalex.org/W4389159523","https://openalex.org/W4411572975","https://openalex.org/W2540833380","https://openalex.org/W4221030495","https://openalex.org/W3132127071","https://openalex.org/W4225395015"],"abstract_inverted_index":{"Here":[0],"you":[1],"will":[2],"find":[3],"all":[4],"the":[5,12,61],"data,":[6],"code,":[7],"and":[8,28,48,66,82],"analysis":[9],"used":[10],"for":[11,84],"scifer":[13,15],"manuscript.":[14],"is":[16],"an":[17],"R/Bioconductor":[18],"package":[19],"that":[20],"can":[21,35],"preprocess":[22],"raw":[23,29],"data":[24],"from":[25],"index":[26],"sorts":[27],"BCR":[30],"Sanger":[31],"sequencing":[32],"data.":[33],"It":[34],"identify":[36],"high-quality":[37],"sequences":[38],"based":[39],"on":[40],"different":[41],"parameters,":[42],"such":[43],"as":[44],"length,":[45],"Phred":[46],"scores,":[47],"heavy-chain":[49],"complementarity-determining":[50],"region":[51],"3":[52],"(HCDR3)":[53],"quality.":[54],"As":[55],"a":[56],"result,":[57],"it":[58],"significantly":[59],"increases":[60],"quality":[62,75],"of":[63],"germline":[64],"assignments":[65],"reduces":[67],"spurious":[68],"variable":[69],"gene":[70],"mutations.":[71],"Its":[72],"output":[73],"provides":[74],"control":[76],"reports,":[77],"FASTA":[78],"files,":[79],"summarized":[80],"tables,":[81],"electropherograms":[83],"manual":[85],"inspection.":[86]},"counts_by_year":[],"updated_date":"2026-10-27T15:51:10.671819","created_date":"2023-10-03T00:00:00"}