{"id":"https://openalex.org/W7204274268","doi":"https://doi.org/10.5281/zenodo.22113955","title":"aertslab/CREsted: 1.1.0","display_name":"aertslab/CREsted: 1.1.0","publication_year":2024,"publication_date":"2024-10-11","ids":{"openalex":"https://openalex.org/W7204274268","doi":"https://doi.org/10.5281/zenodo.22113955"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.22113955","doi":"https://doi.org/10.5281/zenodo.22113955","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22113955","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":"Software"},"volume":null,"type":"software","is_traditional":false,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.22113955","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5148212459","display_name":"Cas Blaauw","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cas Blaauw","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148179549","display_name":"Lukas Mahieu","orcid":"https://orcid.org/0009-0002-5085-6985","observed_orcids":["https://orcid.org/0009-0002-5085-6985"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lukas Mahieu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093400185","display_name":"Niklas Kempynck","orcid":"https://orcid.org/0000-0002-0104-4844","observed_orcids":["https://orcid.org/0000-0002-0104-4844"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Niklas Kempynck","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039340595","display_name":"Seppe De Winter","orcid":"https://orcid.org/0000-0001-7907-1247","observed_orcids":["https://orcid.org/0000-0001-7907-1247"]},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Seppe De Winter","raw_affiliation_strings":["KULeuven"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KULeuven","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093472327","display_name":"Eren Can Ek\u015fi","orcid":"https://orcid.org/0000-0002-3122-9858","observed_orcids":["https://orcid.org/0000-0002-3122-9858"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eren Can Eksi","raw_affiliation_strings":["@aertslab"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"@aertslab","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137311399","display_name":"Gert Hulselmans","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gert Hulselmans","raw_affiliation_strings":["@aertslab"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"@aertslab","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148211829","display_name":"Vasileios Konstantakos","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vasileios Konstantakos","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148348374","display_name":"AntonDeBrabandere","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"AntonDeBrabandere","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148332551","display_name":"Sam","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405260244","display_name":"VIB.AI","ror":"https://ror.org/03fds3g42","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4405260244"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Sam","raw_affiliation_strings":["VIB.AI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VIB.AI","institution_ids":["https://openalex.org/I4405260244"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148404593","display_name":"KUL-SeppeDeWinter","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"KUL-SeppeDeWinter","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122927599","display_name":"Camiel Mannens","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Camiel Mannens","raw_affiliation_strings":["VIB"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"VIB","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5148208448","display_name":"scverse-bot","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"scverse-bot","raw_affiliation_strings":["@scverse"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"@scverse","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.95169997215271,"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":0.95169997215271,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.005100000184029341,"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":0.002400000113993883,"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/deep-learning","display_name":"deep learning","score":0.32600000500679016},{"id":"https://openalex.org/keywords/transfer-learning","display_name":"transfer learning","score":0.5690000057220459},{"id":"https://openalex.org/keywords/bigwig-files","display_name":"bigWig files","score":0.546999990940094},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"pattern matching","score":0.43299999833106995},{"id":"https://openalex.org/keywords/tomato","display_name":"tomato","score":0.375},{"id":"https://openalex.org/keywords/one-hot-encoding","display_name":"one-hot encoding","score":0.4569999873638153}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.629800021648407},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5857999920845032},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5097000002861023},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5026999711990356},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.43849998712539673},{"id":"https://openalex.org/C2781238097","wikidata":"https://www.wikidata.org/wiki/Q175026","display_name":"Object (grammar)","level":2,"score":0.41659998893737793},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.39800000190734863},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.3921000063419342},{"id":"https://openalex.org/C2780428219","wikidata":"https://www.wikidata.org/wiki/Q16952335","display_name":"Cover (algebra)","level":2,"score":0.3772999942302704},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35019999742507935},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.33889999985694885},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.336899995803833},{"id":"https://openalex.org/C2779227376","wikidata":"https://www.wikidata.org/wiki/Q6505497","display_name":"Layer (electronics)","level":2,"score":0.3278999924659729},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3192000091075897},{"id":"https://openalex.org/C167651023","wikidata":"https://www.wikidata.org/wiki/Q1474611","display_name":"Plot (graphics)","level":2,"score":0.2854999899864197},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.28220000863075256},{"id":"https://openalex.org/C199639397","wikidata":"https://www.wikidata.org/wiki/Q1788588","display_name":"Engineering drawing","level":1,"score":0.2809999883174896},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26330000162124634},{"id":"https://openalex.org/C2776245389","wikidata":"https://www.wikidata.org/wiki/Q962139","display_name":"Programming style","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2533999979496002},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25040000677108765}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.22113955","doi":"https://doi.org/10.5281/zenodo.22113955","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22113955","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":"Software"},{"id":"doi:10.5281/zenodo.22113956","doi":"https://doi.org/10.5281/zenodo.22113956","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22113956","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":"Software"}],"best_oa_location":{"id":"doi:10.5281/zenodo.22113955","doi":"https://doi.org/10.5281/zenodo.22113955","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22113955","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":"Software"},"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/W7204243678","https://openalex.org/W7202149651","https://openalex.org/W6894020013","https://openalex.org/W7222346646"],"abstract_inverted_index":{"1.1.0":[0],"Features":[1],"enhancer":[2,16,23,99],"design":[3],"plotting":[4],"and":[5,150,172],"calculation":[6,86],"functions":[7,37,62,149],"in":[8,26,33,40,51,60,68,88,134],"the":[9,111,122],"crested.tl.Crested":[10,69],"object":[11],"new":[12,20,28,96,98],"module":[13],"crested.tl.modisco":[14,159],"with":[15,78,95],"code":[17,24,100,144],"analysis":[18,25,101],"functionality":[19,97,156],"plots":[21],"for":[22,30,76,127,139],"crested.pl.patterns":[27],"plot":[29],"sequence":[31],"prediction":[32],"crested.pl.bar":[34],"hidden":[35],"utility":[36,71,83,148],"now":[38,49,108,166],"public":[39],"crested.utils":[41,154],"(such":[42],"as":[43],"one":[44],"hot":[45],"encoding)":[46],"CosineMSELog":[47],"loss":[48],"default":[50],"peak_regression":[52],"configs":[53],"instead":[54,124],"of":[55,125],"CosineMSE":[56],"tangermeme":[57],"tomtom":[58],"option":[59],"tfmodisco":[61,155],"get_embeddings":[63],"based":[64],"on":[65,168,176],"layer":[66],"name":[67],"crested.utils.EnhancerOptimizer":[70],"function":[72,107],"crested.utils.permute_model":[73],"utility,":[74],"useful":[75],"using":[77],"other":[79],"toch":[80],"packages":[81],"crested.utils.extract_bigwig_values_per_bp":[82],"improved":[84],"correlation":[85],"speed":[87],"heatmaps":[89],"Tutorials":[90],"introductory":[91],"notebook":[92],"is":[93],"updated":[94],"tutorial":[102],"Bug":[103],"Fixes":[104],"transfer":[105],"Learning":[106],"doesn't":[109],"expect":[110],"dense":[112],"block":[113],"anymore":[114],"bigwigs":[115],"importing":[116,136],"checks":[117,165],"if":[118],"it":[119],"can":[120],"open":[121],"file":[123],"looking":[126],".bw":[128],"extension":[129],"no":[130],"more":[131],"ambiguous":[132],"names":[133],"bed":[135],"version":[137],"requirement":[138],"modiscolite":[140],"general":[141,161],"pattern":[142],"matching":[143],"bugfixes":[145],"Breaking":[146],"Changes":[147],"logging":[151],"moved":[152,157],"to":[153,158],"Other":[160],"documentation":[162],"fixes":[163],"style":[164],"enforced":[167],"push":[169,177],"both":[170],"tf":[171],"torch":[173],"backend":[174],"tests":[175]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-08-27T00:00:00"}