{"Package":"quincunx","Type":"Package","Title":"REST API Client for the 'PGS' Catalog","Version":"0.1.7","Authors@R":"c(\nperson(given = \"Ramiro\", family = \"Magno\",\nemail = \"rmagno@pattern.institute\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5226-3441\")),\nperson(given = \"Isabel\", family = \"Duarte\",\nemail = \"iduarte.scientist@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-0060-2936\")),\nperson(given = \"Ana-Teresa\", family = \"Maia\",\nemail = \"maia.anateresa@gmail.com\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0454-9207\")),\nperson(\"CINTESIS\", role = c(\"cph\", \"fnd\")),\nperson(\"Pattern Institute\", role = c(\"cph\", \"fnd\"))\n)","Description":"Programmatic access to the 'PGS' Catalog.\nThis package provides easy access to 'PGS' Catalog data by\naccessing the REST API .","License":"MIT + file LICENSE","Encoding":"UTF-8","LazyData":"true","RoxygenNote":"7.2.3","Suggests":"testthat, knitr, rmarkdown, ggplot2","Imports":"stringr, magrittr, vroom, purrr, glue, dplyr, tidyjson,\ntibble, lubridate, rlang, tidyr, httr, utils, rvest, progress,\nmethods, writexl, concatenate, memoise","Collate":"'ancestry_categories.R' 'class-cohorts.R'\n'class-performance_metrics.R' 'class-publications.R'\n'class-releases.R' 'class-sample_sets.R' 'class-scores.R'\n'class-trait_categories.R' 'class-traits.R' 'clear_cache.R'\n'contains_question_mark.R' 'count.R' 'drop_metadata_cols.R'\n'first_non_na.R' 'generics.R' 'get.R'\n'get_ancestry_categories.R' 'get_cohorts.R' 'get_column.R'\n'get_performance_metrics.R' 'get_publications.R'\n'get_releases.R' 'get_sample_sets.R' 'get_scores.R'\n'get_trait_categories.R' 'get_traits.R' 'id_mapping.R'\n'is_json_empty.R' 'is_paginated.R' 'is_pgs_id.R'\n'is_pubmed_id.R' 'messages.R' 'n_pages.R' 'nr_to_na.R'\n'offsets.R' 'open_in_dbsnp.R' 'open_in_pgs_catalog.R'\n'open_in_pubmed.R' 'parse-ancestry_categories.R'\n'parse-cohorts.R' 'parse-performance_metrics.R'\n'parse-publications.R' 'parse-releases.R' 'parse-sample_sets.R'\n'parse-scores.R' 'parse-trait_categories.R' 'parse-traits.R'\n'read_file_column_names.R' 'read_pgs_scoring_file.R'\n'relocate_metadata_cols.R' 'remap_id.R' 'request.R'\n's4-utils.R' 'stages.R' 'sure.R' 'unwrap_cohort.R'\n'unwrap_demographics.R' 'unwrap_efotrait.R' 'unwrap_interval.R'\n'unwrap_publication.R' 'unwrap_sample.R' 'utils-pipe.R'\n'warnings.R' 'write_xlsx.R'","Depends":"R (>= 2.10)","URL":"https://github.com/ramiromagno/quincunx,\nhttps://rmagno.eu/quincunx/","BugReports":"https://github.com/ramiromagno/quincunx/issues","NeedsCompilation":"no","Packaged":"2023-07-04 16:06:47 UTC; rmagno","Author":"Ramiro Magno [aut, cre] (),\nIsabel Duarte [aut] (),\nAna-Teresa Maia [aut] (),\nCINTESIS [cph, fnd],\nPattern Institute [cph, fnd]","Maintainer":"Ramiro Magno ","Repository":"CRAN","Date/Publication":"2023-07-04 16:20:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/quincunx_0.1.7.tar.gz","jsonAuthors":[{"name":"Ramiro Magno","email":"rmagno@pattern.institute","maintainer":true},{"name":"Isabel Duarte","email":"iduarte.scientist@gmail.com","maintainer":false},{"name":"Ana-Teresa Maia","email":"maia.anateresa@gmail.com","maintainer":false},{"name":"CINTESIS ","email":null,"maintainer":false},{"name":"Pattern Institute ","email":null,"maintainer":false}],"readme":"\n\n\n# quincunx

\n\n\n\n[![CRAN\nstatus](https://www.r-pkg.org/badges/version/quincunx)](https://CRAN.R-project.org/package=quincunx)\n[![License:\nMIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)\n[![lifecycle](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![](https://img.shields.io/badge/doi-10.1093/bioinformatics/btab522-blue.svg)](https://doi.org/10.1093/bioinformatics/btab522)\n\n\nThe goal of `{quincunx}` is to provide programmatic access to the\n[Polygenic Score (PGS) Catalog](https://www.pgscatalog.org/), an open\nresource for [polygenic\nscores](https://en.wikipedia.org/wiki/Polygenic_score) and associated\nmetadata describing their development and respective assessment.\n\nBrowse the online documentation at\n[rmagno.eu/quincunx](https://rmagno.eu/quincunx/) to get started.\n\n## Installation\n\nInstall `{quincunx}` from CRAN:\n\n``` r\n# Install from CRAN\ninstall.packages(\"quincunx\")\n```\n\nYou can instead install the development version of `{quincunx}` by\nsetting [Ramiro Magno’s universe](https://ramiromagno.r-universe.dev/)\nrepository:\n\n``` r\noptions(repos = c(ramiromagno = 'https://ramiromagno.r-universe.dev',\n CRAN = 'https://cloud.r-project.org'))\n\ninstall.packages('quincunx')\n```\n\n## Cheatsheet\n\n

\n\n## Citing this work\n\n`{quincunx}` was published in Bioinformatics in 2021:\n.\n\nTo generate a citation for this publication from within R:\n\n``` r\ncitation('quincunx')\n#> \n#> To cite quincunx in publications use:\n#> \n#> Ramiro Magno, Isabel Duarte, Ana-Teresa Maia, quincunx: an R package\n#> to query, download and wrangle PGS Catalog data, Bioinformatics,\n#> btab522, 16 July 2021, Pages 1-3,\n#> https://doi.org/10.1093/bioinformatics/btab522\n#> \n#> A BibTeX entry for LaTeX users is\n#> \n#> @Article{,\n#> title = {quincunx: an R package to query, download and wrangle PGS Catalog data},\n#> author = {Ramiro Magno and Isabel Duarte and Ana-Teresa Maia},\n#> journal = {Bioinformatics},\n#> year = {2021},\n#> pages = {1--3},\n#> url = {https://doi.org/10.1093/bioinformatics/btab522},\n#> }\n```\n\n## Citing PGS Catalog publications\n\nAlso, please do not forget to cite the authors behind the original\nstudies and the papers associated with the PGS Catalog project:\n\n- Lambert, S.A., Gil, L., Jupp, S. et al. The Polygenic Score Catalog as\n an open database for reproducibility and systematic evaluation. Nat\n Genet 53, 420–425 (2021). doi:\n [10.1038/s41588-021-00783-5](https://doi.org/10.1038/s41588-021-00783-5)\n- Wand, H., Lambert, S.A., Tamburro, C. et al. Improving reporting\n standards for polygenic scores in risk prediction studies. Nature 591,\n 211–219 (2021). doi:\n [10.1038/s41586-021-03243-6](https://doi.org/10.1038/s41586-021-03243-6)\n\n## Terms of use\n\nPlease note that if you use the data provided by the PGS Catalog either\ndirectly or via `{quincunx}` you agree to abide to the [EMBL-EBI Terms\nof Use](https://www.ebi.ac.uk/about/terms-of-use/).\n\n## Code of Conduct\n\nPlease note that the `{quincunx`} project is released with a\n[Contributor Code of\nConduct](https://rmagno.eu/quincunx/CODE_OF_CONDUCT.html). By\ncontributing to this project, you agree to abide by its terms.\n\n## Acknowledgements\n\nThis work would have not been possible without the precious feedback\nfrom the [PGS Catalog team](https://www.pgscatalog.org/), particularly\n[Samuel Lambert](https://www.ebi.ac.uk/about/people/samuel-lambert) and\n[Laurent Gil](https://www.sanger.ac.uk/person/gil-laurent/).\n\n## Package name and hex sticker\n\nThe package name `{quincunx}` is another name for [Galton\nBoard](https://en.wikipedia.org/wiki/Bean_machine), that so nicely\nexemplifies the [Central Limit\nTheorem](https://en.wikipedia.org/wiki/Central_limit_theorem), which in\nturn is a key concept of genetics, namely, [Fisher’s infinitesimal\nmodel](https://doi.org/10.1016/j.tpb.2017.09.003)… which leads us to\nPolygenic Scores, the key concept of the PGS Catalog.\n\nThe bird in the hex sticker is a *Porphyrio porphyrio*, an emblematic\nspecies native to the Ria Formosa Natural Park, which is a wildlife\nreserve surrounding the University of Algarve, where the authors are\naffiliated.","jobInfo":{"package":"quincunx","version":"0.1.7","parsingStatus":"success","parserVersion":2,"parsedAt":"2025-03-20T17:30:08+0000"}}

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