{"id":"https://openalex.org/W2134916359","doi":"https://doi.org/10.1186/s12859-015-0742-6","title":"methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data","display_name":"methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data","publication_year":2015,"publication_date":"2015-09-28","ids":{"openalex":"https://openalex.org/W2134916359","doi":"https://doi.org/10.1186/s12859-015-0742-6","mag":"2134916359","pmid":"https://pubmed.ncbi.nlm.nih.gov/26415965"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0742-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0742-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0742-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0742-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045178955","display_name":"Kamal Kishore","orcid":"https://orcid.org/0000-0002-4650-8745"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Kamal Kishore","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. kamal.kishore@iit.it","Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. kamal.kishore@iit.it","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy","institution_ids":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030744275","display_name":"Stefano de Pretis","orcid":"https://orcid.org/0000-0003-1103-7688"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano de Pretis","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. stefano.depretis@iit.it","Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. stefano.depretis@iit.it","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy","institution_ids":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057408603","display_name":"Ryan Lister","orcid":"https://orcid.org/0000-0001-6637-7239"},"institutions":[{"id":"https://openalex.org/I1307098950","display_name":"Salk Institute for Biological Studies","ror":"https://ror.org/03xez1567","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1307098950"]},{"id":"https://openalex.org/I1337719021","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86","country_code":"AU","type":"government","lineage":["https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210132349"]},{"id":"https://openalex.org/I177877127","display_name":"The University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]},{"id":"https://openalex.org/I4210102918","display_name":"ARC Centre of Excellence in Plant Energy Biology","ror":"https://ror.org/01a1mq059","country_code":"AU","type":"facility","lineage":["https://openalex.org/I118347636","https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210102918","https://openalex.org/I4210132349"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Ryan Lister","raw_affiliation_strings":["Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia. ryan.lister@uwa.edu.au","Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ryan.lister@uwa.edu.au","Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia. ryan.lister@uwa.edu.au","institution_ids":["https://openalex.org/I1337719021","https://openalex.org/I4210102918"]},{"raw_affiliation_string":"Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ryan.lister@uwa.edu.au","institution_ids":["https://openalex.org/I1307098950"]},{"raw_affiliation_string":"Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia","institution_ids":["https://openalex.org/I1337719021","https://openalex.org/I177877127"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007690571","display_name":"Marco J. Morelli","orcid":"https://orcid.org/0000-0003-1862-667X"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco J. Morelli","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. marco.morelli@iit.it","Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. marco.morelli@iit.it","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy","institution_ids":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085896954","display_name":"Valerio Bianchi","orcid":"https://orcid.org/0000-0001-9025-7923"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Valerio Bianchi","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. valerio.bianchi@iit.it","Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. valerio.bianchi@iit.it","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy","institution_ids":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036162019","display_name":"Bruno Amati","orcid":"https://orcid.org/0000-0002-2958-1799"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]},{"id":"https://openalex.org/I6141010","display_name":"European Institute of Oncology","ror":"https://ror.org/02vr0ne26","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I6141010"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Bruno Amati","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. bruno.amati@iit.it","Department of Experimental Oncology, European Institute of Oncology (IEO), Milano, 20139, Italy. bruno.amati@iit.it","Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. bruno.amati@iit.it","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Department of Experimental Oncology, European Institute of Oncology (IEO), Milano, 20139, Italy. bruno.amati@iit.it","institution_ids":["https://openalex.org/I6141010"]},{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy","institution_ids":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035293995","display_name":"Joseph R. Ecker","orcid":"https://orcid.org/0000-0001-5799-5895"},"institutions":[{"id":"https://openalex.org/I1307098950","display_name":"Salk Institute for Biological Studies","ror":"https://ror.org/03xez1567","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1307098950"]},{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joseph R. Ecker","raw_affiliation_strings":["Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ecker@salk.edu","Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ecker@salk.edu","Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ecker@salk.edu","institution_ids":["https://openalex.org/I1307098950"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. ecker@salk.edu","institution_ids":["https://openalex.org/I1307098950","https://openalex.org/I1344073410"]},{"raw_affiliation_string":"Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA","institution_ids":["https://openalex.org/I1307098950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012974572","display_name":"Mattia Pelizzola","orcid":"https://orcid.org/0000-0001-6672-9636"},"institutions":[{"id":"https://openalex.org/I1307098950","display_name":"Salk Institute for Biological Studies","ror":"https://ror.org/03xez1567","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1307098950"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT","US"],"is_corresponding":true,"raw_author_name":"Mattia Pelizzola","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. mattia.pelizzola@iit.it","Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. mattia.pelizzola@iit.it","Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milano, 20139, Italy. mattia.pelizzola@iit.it","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. mattia.pelizzola@iit.it","institution_ids":["https://openalex.org/I1307098950"]},{"raw_affiliation_string":"Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA","institution_ids":["https://openalex.org/I1307098950"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5012974572","https://openalex.org/A5035293995"],"corresponding_institution_ids":["https://openalex.org/I1307098950","https://openalex.org/I1344073410","https://openalex.org/I30771326"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":3.3018,"has_fulltext":true,"cited_by_count":73,"citation_normalized_percentile":{"value":0.92953545,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"313","last_page":"313"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9156000018119812,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9156000018119812,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.031099999323487282,"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/T11482","display_name":"RNA modifications and cancer","score":0.021900000050663948,"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":0.8802729845046997},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.8323708176612854},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5872722268104553},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.580394983291626},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.56960529088974},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5198208093643188},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4552451968193054},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.44819512963294983},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4206121563911438},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39575228095054626},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.35094907879829407},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.347587525844574},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26329463720321655},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14854970574378967}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8802729845046997},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.8323708176612854},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5872722268104553},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.580394983291626},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.56960529088974},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5198208093643188},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4552451968193054},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.44819512963294983},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4206121563911438},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39575228095054626},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.35094907879829407},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.347587525844574},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26329463720321655},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14854970574378967},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-015-0742-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0742-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0742-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pure.atira.dk:openaire/2dab93a6-dd8e-4361-b11f-75c6e095a2ea","is_oa":true,"landing_page_url":"https://research-repository.uwa.edu.au/en/publications/2dab93a6-dd8e-4361-b11f-75c6e095a2ea","pdf_url":null,"source":{"id":"https://openalex.org/S4306402492","display_name":"UWA Profiles and Research Repository (UWA)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177877127","host_organization_name":"The University of Western Australia","host_organization_lineage":["https://openalex.org/I177877127"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Kishore, K, De Pretis, S, Lister, R, Morelli, M J, Bianchi, V, Amati, B, Ecker, J R & Pelizzola, M 2015, 'methylPipe and compEpiTools: A suite of R packages for the integrative analysis of epigenomics data', BMC Bioinformatics, vol. 16, no. 1, pp. 1-11. https://doi.org/10.1186/s12859-015-0742-6","raw_type":"info:eu-repo/semantics/article"},{"id":"pmid:26415965","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26415965","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4587815","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4587815","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:boa.unimib.it:10281/446698","is_oa":true,"landing_page_url":"https://hdl.handle.net/10281/446698","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0742-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0742-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0742-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1007191511","display_name":null,"funder_award_id":"U01 ES017166","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G2905292489","display_name":null,"funder_award_id":"1U01MH105985","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G2973790809","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4683282134","display_name":null,"funder_award_id":"U01 MH105985","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G5730444723","display_name":null,"funder_award_id":"305626","funder_id":"https://openalex.org/F4320334960","funder_display_name":"Seventh Framework Programme"},{"id":"https://openalex.org/G680976502","display_name":null,"funder_award_id":"P30 CA-014195","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306202","display_name":"Gordon and Betty Moore Foundation","ror":"https://ror.org/006wxqw41"},{"id":"https://openalex.org/F4320306644","display_name":"Mary K. Chapman Foundation","ror":"https://ror.org/01x8qsj42"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334960","display_name":"Seventh Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2134916359.pdf","grobid_xml":"https://content.openalex.org/works/W2134916359.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1963590871","https://openalex.org/W1967841068","https://openalex.org/W1977371925","https://openalex.org/W1979273476","https://openalex.org/W1979513200","https://openalex.org/W1979674827","https://openalex.org/W2001964616","https://openalex.org/W2014852291","https://openalex.org/W2019229253","https://openalex.org/W2028839461","https://openalex.org/W2032882684","https://openalex.org/W2036124215","https://openalex.org/W2049907774","https://openalex.org/W2059099579","https://openalex.org/W2067151470","https://openalex.org/W2074022199","https://openalex.org/W2076498407","https://openalex.org/W2078025753","https://openalex.org/W2105300601","https://openalex.org/W2107457596","https://openalex.org/W2110017531","https://openalex.org/W2112988834","https://openalex.org/W2117675660","https://openalex.org/W2124748744","https://openalex.org/W2124952135","https://openalex.org/W2131374955","https://openalex.org/W2131478115","https://openalex.org/W2135229538","https://openalex.org/W2142386149","https://openalex.org/W2146577751","https://openalex.org/W2146862337","https://openalex.org/W2150194502","https://openalex.org/W2150936392","https://openalex.org/W2154906308","https://openalex.org/W2156124720","https://openalex.org/W2156408641","https://openalex.org/W2158320325","https://openalex.org/W2160697532","https://openalex.org/W2161224111","https://openalex.org/W2161435642","https://openalex.org/W2161645441","https://openalex.org/W2168031748","https://openalex.org/W2168810759","https://openalex.org/W2914577469"],"related_works":["https://openalex.org/W2946746360","https://openalex.org/W2592564295","https://openalex.org/W2606237140","https://openalex.org/W2100856525","https://openalex.org/W2119272378","https://openalex.org/W1499793237","https://openalex.org/W3035076328","https://openalex.org/W3119866144","https://openalex.org/W2151651283","https://openalex.org/W2044676948"],"abstract_inverted_index":{"BACKGROUND:":[0],"Numerous":[1],"methods":[2,190],"are":[3,21,64,279],"available":[4,101],"to":[5,74,127,191,200],"profile":[6],"several":[7,137],"epigenetic":[8],"marks,":[9,78],"providing":[10,282],"data":[11,84,95,111,194,249,258],"with":[12,27,86,99,113,175,181,230,254,284],"different":[13],"genome":[14],"coverage":[15],"and":[16,24,39,72,81,96,144,177,206,215,223,262],"resolution.":[17],"Large":[18],"epigenomic":[19],"datasets":[20],"then":[22],"generated,":[23],"often":[25],"combined":[26,73],"other":[28,82,182],"high-throughput":[29],"data,":[30,56,89,297],"including":[31],"RNA-seq,":[32],"ChIP-seq":[33],"for":[34,60,244,269],"transcription":[35],"factors":[36],"(TFs)":[37],"binding":[38,80],"DNase-seq":[40],"experiments.":[41],"Despite":[42],"the":[43,51,91,106,128,160,172,201,219,224,227,235,245,270,292,301],"numerous":[44],"computational":[45],"tools":[46,68],"covering":[47],"specific":[48],"steps":[49],"in":[50,136,141,195,281,299],"analysis":[52,63,92,129,149,272,293],"of":[53,93,108,130,150,162,189,197,203,218,226,247,273,294],"large-scale":[54],"epigenomics":[55,183,275],"comprehensive":[57,216,266],"software":[58],"solutions":[59],"their":[61,97,179,295],"integrative":[62,271],"still":[65],"missing.":[66],"Multiple":[67],"must":[69],"be":[70],"identified":[71],"jointly":[75],"analyze":[76],"histone":[77],"TFs":[79],"-omics":[83],"together":[85],"DNA":[87,134],"methylation":[88],"complicating":[90],"these":[94,193],"integration":[98,180,246],"publicly":[100],"datasets.":[102],"RESULTS:":[103],"To":[104],"overcome":[105],"burden":[107],"integrating":[109,163],"various":[110,248],"types":[112],"multiple":[114,151],"tools,":[115],"we":[116],"developed":[117],"two":[118],"companion":[119],"R/Bioconductor":[120],"packages.":[121],"The":[122,148,167],"former,":[123],"methylPipe,":[124],"is":[125,156],"tailored":[126],"high-":[131],"or":[132,256,298],"low-resolution":[133],"methylomes":[135],"species,":[138],"accommodating":[139],"(hydroxy-)methyl-cytosines":[140],"both":[142],"CpG":[143],"non-CpG":[145],"sequence":[146],"context.":[147],"whole-genome":[152],"bisulfite":[153],"sequencing":[154],"experiments":[155],"supported,":[157],"while":[158],"maintaining":[159],"ability":[161],"targeted":[164],"genomic":[165,221],"data.":[166,184,276],"latter,":[168],"compEpiTools,":[169],"seamlessly":[170],"incorporates":[171],"results":[173],"obtained":[174],"methylPipe":[176,261],"supports":[178],"It":[185],"provides":[186],"a":[187,213,238,265,288],"number":[188],"score":[192],"regions":[196],"interest,":[198],"leading":[199],"identification":[202],"enhancers,":[204],"lncRNAs,":[205],"RNAPII":[207],"stalling/elongation":[208],"dynamics.":[209],"Moreover,":[210],"it":[211],"allows":[212],"fast":[214],"annotation":[217,252],"resulting":[220],"regions,":[222],"association":[225],"corresponding":[228],"genes":[229],"non-redundant":[231],"GeneOntology":[232],"terms.":[233],"Finally,":[234],"package":[236],"includes":[237],"flexible":[239],"method":[240],"based":[241],"on":[242],"heatmaps":[243],"types,":[250],"combining":[251],"tracks":[253],"continuous":[255],"categorical":[257],"tracks.":[259],"CONCLUSIONS:":[260],"compEpiTools":[263],"provide":[264],"Bioconductor-compliant":[267],"solution":[268],"heterogeneous":[274],"These":[277],"packages":[278],"instrumental":[280],"biologists":[283],"minimal":[285],"R":[286],"skills":[287],"complete":[289],"toolkit":[290],"facilitating":[291],"own":[296],"accelerating":[300],"analyses":[302],"performed":[303],"by":[304],"more":[305],"experienced":[306],"bioinformaticians.":[307]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-12T07:12:00.856984","created_date":"2025-10-10T00:00:00"}