{"id":"https://openalex.org/W2969009138","doi":"https://doi.org/10.7490/f1000research.1117187.1","title":"DASA: a computational pipeline for differential ATAC-Seq analysis","display_name":"DASA: a computational pipeline for differential ATAC-Seq analysis","publication_year":2019,"publication_date":"2019-07-30","ids":{"openalex":"https://openalex.org/W2969009138","doi":"https://doi.org/10.7490/f1000research.1117187.1","mag":"2969009138"},"language":"en","primary_location":{"id":"doi:10.7490/f1000research.1117187.1","doi":"https://doi.org/10.7490/f1000research.1117187.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1117187.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"other","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7490/f1000research.1117187.1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012026856","display_name":"Alberto Riva","orcid":"https://orcid.org/0000-0001-9150-8333","observed_orcids":["https://orcid.org/0000-0001-9150-8333"]},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alberto Riva","raw_affiliation_strings":["University of Florida, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Florida, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008754012","display_name":"Richard Lynn Bennett","orcid":"https://orcid.org/0000-0002-0243-2443","observed_orcids":["https://orcid.org/0000-0002-0243-2443"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Richard L Bennett","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027282023","display_name":"Kartika Venugopal","orcid":"https://orcid.org/0000-0002-3202-2621","observed_orcids":["https://orcid.org/0000-0002-3202-2621"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kartika Venugopal","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014754069","display_name":"Olga A. Guryanova","orcid":"https://orcid.org/0000-0002-6514-8466","observed_orcids":["https://orcid.org/0000-0002-6514-8466","https://orcid.org/0000-0003-4974-3166"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Olga Guryanova","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013666609","display_name":"Jason Orr Brant","orcid":"https://orcid.org/0000-0002-9800-9251","observed_orcids":["https://orcid.org/0000-0002-9800-9251"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jason O Brant","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5034992183","display_name":"Jonathan D. Licht","orcid":"https://orcid.org/0000-0002-3942-1369","observed_orcids":["https://orcid.org/0000-0002-3942-1369"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jonathan D Licht","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012026856"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"8","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9765999913215637,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9765999913215637,"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/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.01080000028014183,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.00139999995008111,"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/chromatin-accessibility","display_name":"chromatin accessibility","score":0.9900000095367432},{"id":"https://openalex.org/keywords/peak-calling","display_name":"peak calling","score":0.7429999709129333},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.550000011920929},{"id":"https://openalex.org/keywords/genome-browser-tracks","display_name":"genome browser tracks","score":0.6959999799728394}],"concepts":[{"id":"https://openalex.org/C2983643791","wikidata":"https://www.wikidata.org/wiki/Q1999993","display_name":"Open peer review","level":3,"score":0.8473879098892212},{"id":"https://openalex.org/C2992936677","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Plant biology","level":2,"score":0.7018030881881714},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6578540205955505},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5573889017105103},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.48268890380859375},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.39047449827194214},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37620094418525696},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.3350992202758789},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33484262228012085},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.13487112522125244},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.09433916211128235},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.04609018564224243},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.7490/f1000research.1117187.1","doi":"https://doi.org/10.7490/f1000research.1117187.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1117187.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"doi:10.7490/f1000research.1117187.1","doi":"https://doi.org/10.7490/f1000research.1117187.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1117187.1","pdf_url":null,"source":{"id":"https://openalex.org/S7407050752","display_name":"Faculty of 1000 Research Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Other"},{"id":"mag:2969009138","doi":null,"is_oa":true,"landing_page_url":"https://f1000research.com/posters/8-1257","pdf_url":null,"source":{"id":"https://openalex.org/S4210239046","display_name":"F1000Research","issn_l":"2046-1402","issn":["2046-1402"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320357","host_organization_name":"Faculty of 1000","host_organization_lineage":["https://openalex.org/P4310320357","https://openalex.org/P4310320547"],"host_organization_lineage_names":["Faculty of 1000","Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":"F1000Research","raw_type":null}],"best_oa_location":{"id":"doi:10.7490/f1000research.1117187.1","doi":"https://doi.org/10.7490/f1000research.1117187.1","is_oa":true,"landing_page_url":"https://doi.org/10.7490/f1000research.1117187.1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7127612916","https://openalex.org/W2980454008","https://openalex.org/W4317436506","https://openalex.org/W3036495102","https://openalex.org/W4415514034","https://openalex.org/W7221459651","https://openalex.org/W2792006949","https://openalex.org/W6950783993","https://openalex.org/W3120775643","https://openalex.org/W3132659149"],"abstract_inverted_index":{"ATAC-Seq":[0,21,49,158],"(Assay":[1],"for":[2,156],"Transposase-Accessible":[3],"Chromatin":[4],"with":[5,187],"high-throughput":[6],"Sequencing)":[7],"is":[8,23,94,133,152],"a":[9,95,153,193],"powerful":[10],"method":[11],"to":[12,27,33],"study":[13],"genome-wide":[14],"chromatin":[15,54,65,75],"accessibility.":[16],"Basic":[17],"computational":[18],"analysis":[19,50],"of":[20,45,63,71,87,127,144],"data":[22],"similar":[24],"in":[25,38,167],"principle":[26],"ChIP-seq":[28],"analysis:":[29],"reads":[30,128],"are":[31,181],"aligned":[32],"the":[34,39,43,69,104,111,125,141,145],"genome,":[35],"and":[36,106,139,164,172,175,190],"peaks":[37,90,166,179,186],"alignment":[40,162],"pileup":[41,163],"indicate":[42],"location":[44],"accessible":[46,146],"regions.":[47],"Differential":[48],"aims":[51],"at":[52],"identifying":[53],"accessibility":[55],"differences":[56],"between":[57,91],"two":[58,168],"conditions.":[59],"This":[60],"allows":[61],"detection":[62],"altered":[64],"modification":[66],"signatures,":[67],"or":[68,115],"effect":[70],"mutations":[72],"that":[73,77,180],"disrupt":[74],"structure":[76],"may":[78,108],"have":[79],"profound":[80],"downstream":[81],"effects":[82],"on":[83],"gene":[84],"regulation.":[85],"Identification":[86],"significantly":[88,182],"different":[89],"con-":[92],"ditions":[93],"challenging":[96],"problem.":[97],"Peak":[98],"positions":[99],"must":[100],"be":[101,110],"inferred":[102],"from":[103,161],"data,":[105],"they":[107],"not":[109],"same":[112],"across":[113],"samples":[114],"even":[116],"biological":[117],"replicates.":[118],"The":[119],"most":[120],"commonly":[121],"used":[122],"signal":[123],"measure,":[124],"number":[126],"falling":[129],"inside":[130],"each":[131],"peak,":[132],"affected":[134],"by":[135,140],"total":[136,142],"library":[137],"size":[138,143],"regions,":[147],"requiring":[148],"careful":[149],"normalization.":[150],"DASA":[151,170],"complete":[154,194],"pipeline":[155],"differential":[157,185],"analysis.":[159],"Starting":[160],"called":[165],"conditions,":[169],"identifies":[171],"quantifies":[173],"common":[174],"unique":[176],"peaks,":[177],"finds":[178],"different,":[183],"associates":[184],"nearby":[188],"genes,":[189],"automatically":[191],"generates":[192],"report":[195],"including":[196],"genome":[197],"browser":[198],"tracks.":[199]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2019-08-22T00:00:00"}
