{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039051,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2020,6,24]],"date-time":"2020-06-24T00:00:00Z","timestamp":1592956800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1355406"],"award-info":[{"award-number":["1355406"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipeline that includes both pre-GWAS analysis, such as outlier removal, data transformation and calculation of Best Linear Unbiased Predictions or Best Linear Unbiased Estimates. In addition, post-GWAS analysis, such as haploblock analysis and candidate gene identification, is lacking.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present Holistic Analysis with Pre- and Post-Integration (HAPPI) GWAS, an open-source GWAS tool able to perform pre-GWAS, GWAS and post-GWAS analysis in an automated pipeline using the command-line interface.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>HAPPI GWAS is written in R for any Unix-like operating systems and is available on GitHub (https:\/\/github.com\/Angelovici-Lab\/HAPPI.GWAS.git).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa589","type":"journal-article","created":{"date-parts":[[2020,6,16]],"date-time":"2020-06-16T15:12:00Z","timestamp":1592320320000},"page":"4655-4657","source":"Crossref","is-referenced-by-count":17,"title":["HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6583-0473","authenticated-orcid":false,"given":"Marianne L","family":"Slaten","sequence":"first","affiliation":[{"name":"Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri , Columbia, MO 65211, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3345-9614","authenticated-orcid":false,"given":"Yen On","family":"Chan","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri , Columbia, MO 65211, USA"}]},{"given":"Vivek","family":"Shrestha","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri , Columbia, MO 65211, USA"}]},{"given":"Alexander E","family":"Lipka","sequence":"additional","affiliation":[{"name":"Department of Crop Sciences, University of Illinois , Urbana, IL 61801, USA"}]},{"given":"Ruthie","family":"Angelovici","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, MU Institute for Data Science and Informatics, University of Missouri , Columbia, MO 65211, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,6,24]]},"reference":[{"key":"2023062304264861600_btaa589-B1","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.cell.2016.05.063","article-title":"1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana","volume":"166","author":"Alonso-Blanco","year":"2016","journal-title":"Cell"},{"key":"2023062304264861600_btaa589-B2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","article-title":"Haploview: analysis and visualization of LD and haplotype maps","volume":"21","author":"Barrett","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062304264861600_btaa589-B3","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1111\/j.2517-6161.1964.tb00553.x","article-title":"An analysis of transformations","volume":"26","author":"Box","year":"1964","journal-title":"J. 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