{"id":"https://openalex.org/W2895675303","doi":"https://doi.org/10.1109/tcbb.2018.2873010","title":"Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools","display_name":"Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools","publication_year":2018,"publication_date":"2018-10-10","ids":{"openalex":"https://openalex.org/W2895675303","doi":"https://doi.org/10.1109/tcbb.2018.2873010","mag":"2895675303","pmid":"https://pubmed.ncbi.nlm.nih.gov/30281477"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2873010","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2873010","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046805716","display_name":"Hussain Ahmed Chowdhury","orcid":"https://orcid.org/0000-0002-3872-0308"},"institutions":[{"id":"https://openalex.org/I126601174","display_name":"Tezpur University","ror":"https://ror.org/005x56091","country_code":"IN","type":"education","lineage":["https://openalex.org/I126601174"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Hussain Ahmed Chowdhury","raw_affiliation_strings":["Department of Computer Science and Engineering, Tezpur University, Tezpur, India"],"raw_orcid":"https://orcid.org/0000-0002-3872-0308","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Tezpur University, Tezpur, India","institution_ids":["https://openalex.org/I126601174"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071372272","display_name":"Dhruba K. Bhattacharyya","orcid":"https://orcid.org/0000-0002-9506-7640"},"institutions":[{"id":"https://openalex.org/I126601174","display_name":"Tezpur University","ror":"https://ror.org/005x56091","country_code":"IN","type":"education","lineage":["https://openalex.org/I126601174"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Dhruba Kumar Bhattacharyya","raw_affiliation_strings":["Tezpur University, Tezpur, India","University of Colorado, Denver, USA"],"raw_orcid":"https://orcid.org/0000-0002-9506-7640","affiliations":[{"raw_affiliation_string":"Tezpur University, Tezpur, India","institution_ids":["https://openalex.org/I126601174"]},{"raw_affiliation_string":"University of Colorado, Denver, USA","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049180880","display_name":"Jugal Kalita","orcid":"https://orcid.org/0000-0002-8765-7018"},"institutions":[{"id":"https://openalex.org/I126601174","display_name":"Tezpur University","ror":"https://ror.org/005x56091","country_code":"IN","type":"education","lineage":["https://openalex.org/I126601174"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Jugal Kumar Kalita","raw_affiliation_strings":["Tezpur University, Tezpur, India","University of Colorado, Denver, USA"],"raw_orcid":"https://orcid.org/0000-0002-8765-7018","affiliations":[{"raw_affiliation_string":"Tezpur University, Tezpur, India","institution_ids":["https://openalex.org/I126601174"]},{"raw_affiliation_string":"University of Colorado, Denver, USA","institution_ids":["https://openalex.org/I921990950"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5046805716"],"corresponding_institution_ids":["https://openalex.org/I126601174"],"apc_list":null,"apc_paid":null,"fwci":1.3963,"has_fulltext":false,"cited_by_count":46,"citation_normalized_percentile":{"value":0.81751085,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"17","issue":"2","first_page":"566","last_page":"586"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9976000189781189,"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/T11482","display_name":"RNA modifications and cancer","score":0.9976000189781189,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.729017972946167},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5917651653289795},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5340442061424255},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4533684551715851},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37428849935531616},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3643573522567749},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.3598218560218811},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3303011655807495},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18657657504081726},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1845451295375824},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1306513249874115},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11136338114738464}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.729017972946167},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5917651653289795},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5340442061424255},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4533684551715851},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37428849935531616},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3643573522567749},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3598218560218811},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3303011655807495},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18657657504081726},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1845451295375824},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1306513249874115},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11136338114738464}],"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000592","qualifier_name":"standards","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2018.2873010","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2873010","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30281477","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30281477","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":210,"referenced_works":["https://openalex.org/W1501862196","https://openalex.org/W1569946922","https://openalex.org/W1832436993","https://openalex.org/W1902461024","https://openalex.org/W1952715049","https://openalex.org/W1965917470","https://openalex.org/W1966822396","https://openalex.org/W1968458420","https://openalex.org/W1970156673","https://openalex.org/W1971899779","https://openalex.org/W1973094248","https://openalex.org/W1973276909","https://openalex.org/W1980106585","https://openalex.org/W1981509058","https://openalex.org/W1984708728","https://openalex.org/W1988391018","https://openalex.org/W1994018858","https://openalex.org/W1996370379","https://openalex.org/W1996543077","https://openalex.org/W1999574084","https://openalex.org/W1999768672","https://openalex.org/W2000875411","https://openalex.org/W2011657487","https://openalex.org/W2011920499","https://openalex.org/W2023562174","https://openalex.org/W2024683563","https://openalex.org/W2025648894","https://openalex.org/W2029623390","https://openalex.org/W2035539049","https://openalex.org/W2035618305","https://openalex.org/W2036897871","https://openalex.org/W2038963685","https://openalex.org/W2039521726","https://openalex.org/W2041937775","https://openalex.org/W2048783574","https://openalex.org/W2054576015","https://openalex.org/W2060360855","https://openalex.org/W2061537056","https://openalex.org/W2061912939","https://openalex.org/W2061971803","https://openalex.org/W2062094438","https://openalex.org/W2064469303","https://openalex.org/W2069295116","https://openalex.org/W2070050178","https://openalex.org/W2074414424","https://openalex.org/W2076513103","https://openalex.org/W2077616702","https://openalex.org/W2080837438","https://openalex.org/W2091193685","https://openalex.org/W2093931624","https://openalex.org/W2096192437","https://openalex.org/W2096441981","https://openalex.org/W2096561521","https://openalex.org/W2097065948","https://openalex.org/W2097205777","https://openalex.org/W2097453652","https://openalex.org/W2102278945","https://openalex.org/W2103017472","https://openalex.org/W2103569192","https://openalex.org/W2104005232","https://openalex.org/W2105371278","https://openalex.org/W2107018762","https://openalex.org/W2107060225","https://openalex.org/W2107208863","https://openalex.org/W2107564978","https://openalex.org/W2107665951","https://openalex.org/W2108414900","https://openalex.org/W2109158187","https://openalex.org/W2109288169","https://openalex.org/W2110017531","https://openalex.org/W2110065044","https://openalex.org/W2110392562","https://openalex.org/W2112888168","https://openalex.org/W2112926959","https://openalex.org/W2113312463","https://openalex.org/W2113768712","https://openalex.org/W2114104545","https://openalex.org/W2114405789","https://openalex.org/W2116528446","https://openalex.org/W2117131162","https://openalex.org/W2117688129","https://openalex.org/W2118521406","https://openalex.org/W2121180999","https://openalex.org/W2121211805","https://openalex.org/W2122982115","https://openalex.org/W2123106337","https://openalex.org/W2123579165","https://openalex.org/W2124649657","https://openalex.org/W2124985265","https://openalex.org/W2125258701","https://openalex.org/W2126144698","https://openalex.org/W2126419817","https://openalex.org/W2127284906","https://openalex.org/W2127372456","https://openalex.org/W2128009724","https://openalex.org/W2129202305","https://openalex.org/W2131271579","https://openalex.org/W2132721989","https://openalex.org/W2133465414","https://openalex.org/W2134526812","https://openalex.org/W2136145671","https://openalex.org/W2136453810","https://openalex.org/W2137526110","https://openalex.org/W2137586531","https://openalex.org/W2138207763","https://openalex.org/W2140729960","https://openalex.org/W2143387738","https://openalex.org/W2145416275","https://openalex.org/W2146512944","https://openalex.org/W2148802388","https://openalex.org/W2150491437","https://openalex.org/W2152239989","https://openalex.org/W2152556446","https://openalex.org/W2152710395","https://openalex.org/W2154431984","https://openalex.org/W2154537630","https://openalex.org/W2156631105","https://openalex.org/W2156841387","https://openalex.org/W2156925439","https://openalex.org/W2157710407","https://openalex.org/W2159482845","https://openalex.org/W2159707944","https://openalex.org/W2160443244","https://openalex.org/W2160697532","https://openalex.org/W2161318011","https://openalex.org/W2161488606","https://openalex.org/W2161529001","https://openalex.org/W2162857215","https://openalex.org/W2163296115","https://openalex.org/W2164154943","https://openalex.org/W2165293958","https://openalex.org/W2166558929","https://openalex.org/W2166820820","https://openalex.org/W2168342464","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2174938954","https://openalex.org/W2175981288","https://openalex.org/W2178294617","https://openalex.org/W2179438025","https://openalex.org/W2224056471","https://openalex.org/W2236822143","https://openalex.org/W2261808466","https://openalex.org/W2276982311","https://openalex.org/W2286142055","https://openalex.org/W2288204109","https://openalex.org/W2333113579","https://openalex.org/W2337340335","https://openalex.org/W2409002067","https://openalex.org/W2414843433","https://openalex.org/W2416083568","https://openalex.org/W2418408783","https://openalex.org/W2432815617","https://openalex.org/W2493595287","https://openalex.org/W2507296166","https://openalex.org/W2513413313","https://openalex.org/W2524794421","https://openalex.org/W2527946795","https://openalex.org/W2529694725","https://openalex.org/W2532141416","https://openalex.org/W2567841878","https://openalex.org/W2569381898","https://openalex.org/W2574719153","https://openalex.org/W2577490495","https://openalex.org/W2583708328","https://openalex.org/W2585711475","https://openalex.org/W2586834698","https://openalex.org/W2590817183","https://openalex.org/W2592811885","https://openalex.org/W2595639953","https://openalex.org/W2606232818","https://openalex.org/W2607691714","https://openalex.org/W2610433883","https://openalex.org/W2610537770","https://openalex.org/W2611100408","https://openalex.org/W2614895386","https://openalex.org/W2616922646","https://openalex.org/W2622331767","https://openalex.org/W2624410684","https://openalex.org/W2726891092","https://openalex.org/W2737375639","https://openalex.org/W2746479894","https://openalex.org/W2754041971","https://openalex.org/W2761392474","https://openalex.org/W2780155440","https://openalex.org/W2783975438","https://openalex.org/W2792479311","https://openalex.org/W2794155784","https://openalex.org/W2794521141","https://openalex.org/W2885307522","https://openalex.org/W2949086748","https://openalex.org/W2950985970","https://openalex.org/W2951818953","https://openalex.org/W2952109315","https://openalex.org/W2953067954","https://openalex.org/W3099289621","https://openalex.org/W3103157583","https://openalex.org/W4232483673","https://openalex.org/W4242404314","https://openalex.org/W6638626510","https://openalex.org/W6639743718","https://openalex.org/W6642914199","https://openalex.org/W6676099596","https://openalex.org/W6683504902","https://openalex.org/W6696191187","https://openalex.org/W6716701172","https://openalex.org/W6734069042","https://openalex.org/W6736687592","https://openalex.org/W6737168128","https://openalex.org/W6738649508"],"related_works":["https://openalex.org/W4394359997","https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4362511922","https://openalex.org/W4362485688","https://openalex.org/W4362530184","https://openalex.org/W4362530193","https://openalex.org/W2904597490","https://openalex.org/W4362485661","https://openalex.org/W4394365953"],"abstract_inverted_index":{"Analysis":[0],"of":[1,27,38,44,52,55,60,67,74],"RNA-sequence":[2],"(RNA-seq)":[3],"data":[4,19,46,76,92],"is":[5,62,77],"widely":[6],"used":[7,40],"in":[8,41,69],"transcriptomic":[9],"studies":[10],"and":[11,72,98],"it":[12],"has":[13],"many":[14],"applications.":[15],"We":[16],"review":[17],"RNA-seq":[18,22,45,75,91],"analysis":[20,47],"from":[21],"reads":[23],"to":[24],"the":[25,90],"results":[26],"differential":[28],"expression":[29],"analysis.":[30],"In":[31],"addition,":[32],"we":[33,85],"perform":[34],"a":[35,50],"descriptive":[36],"comparison":[37],"tools":[39,61],"each":[42],"step":[43],"along":[48,80,94],"with":[49,81,95],"discussion":[51,66],"important":[53],"characteristics":[54],"these":[56],"tools.":[57,83],"A":[58,65],"taxonomy":[59],"also":[63,78],"provided.":[64],"issues":[68,97],"quality":[70],"control":[71],"visualization":[73],"included":[79],"useful":[82],"Finally,":[84],"provide":[86],"some":[87],"guidelines":[88],"for":[89],"analyst,":[93],"research":[96],"challenges":[99],"which":[100],"should":[101],"be":[102],"addressed.":[103]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
