From 0d1597b493717975fca97c75034179bd49941adc Mon Sep 17 00:00:00 2001 From: smlmbrt Date: Fri, 4 Oct 2024 11:51:59 +0100 Subject: [PATCH] Update citation to published article --- CITATIONS.md | 6 +++--- README.md | 6 +++--- assets/report/report.qmd | 2 +- docs/explanation/match.rst | 2 +- docs/index.rst | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 7cba0759..b79a4f98 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,6 +1,6 @@ # PGScatalog/pgsc_calc: Citations -> Lambert, Wingfield _et al._ (2024) The Polygenic Score Catalog: new functionality and tools to enable FAIR research. medRxiv. doi:[10.1101/2024.05.29.24307783](https://doi.org/10.1101/2024.05.29.24307783). +> Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x). ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) @@ -13,11 +13,11 @@ ## Pipeline tools * [PGS Catalog API](https://pubmed.ncbi.nlm.nih.gov/33692568/) - > Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 2021 Apr;53(4):420-5. doi: 10.1038/s41588-021-00783-5. PubMed PMID: 33692568. + > Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x). * [pygscatalog](https://github.com/PGScatalog/pygscatalog) - > Lambert, Wingfield _et al._ (2024) The Polygenic Score Catalog: new functionality and tools to enable FAIR research. medRxiv. doi:[10.1101/2024.05.29.24307783](https://doi.org/10.1101/2024.05.29.24307783). + > Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x). * [PLINK 2](https://pubmed.ncbi.nlm.nih.gov/25722852/) > Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015 Dec 1;4(1):s13742-015. doi: 10.1186/s13742-015-0047-8. PubMed PMID: 25722852. PubMed Central PMCID: PMC4342193. diff --git a/README.md b/README.md index 4617e90c..e94455df 100644 --- a/README.md +++ b/README.md @@ -104,9 +104,9 @@ from Aoife McMahon (EBI). Development of new features, testing, and code review is ongoing including Inouye lab members (Rodrigo Canovas, Scott Ritchie) and others. If you use the tool we ask you to cite our paper describing software and updated PGS Catalog resource: -- >Lambert, Wingfield _et al._ (2024) The Polygenic Score Catalog: new functionality - and tools to enable FAIR research. medRxiv. - doi:[10.1101/2024.05.29.24307783](https://doi.org/10.1101/2024.05.29.24307783). +- >Lambert, Wingfield _et al._ (2024) Enhancing the Polygenic Score Catalog with tools for score + calculation and ancestry normalization. Nature Genetics. + doi:[10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x). This pipeline is distrubuted under an [Apache License](LICENSE) amd uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community diff --git a/assets/report/report.qmd b/assets/report/report.qmd index 7a89a128..12b7e171 100644 --- a/assets/report/report.qmd +++ b/assets/report/report.qmd @@ -504,7 +504,7 @@ stringr::str_glue("{params$sampleset}/score/aggregated_scores.txt.gz") > Samuel A. Lambert, Benjamin Wingfield, Joel T. Gibson, Laurent Gil, Santhi Ramachandran, Florent Yvon, Shirin Saverimuttu, Emily Tinsley, Elizabeth Lewis, Scott C. Ritchie, Jingqin Wu, Rodrigo Canovas, Aoife McMahon, Laura W. Harris, Helen Parkinson, Michael Inouye. Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. -Nature Genetics | doi: [10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x) +Nature Genetics (2024) | doi: [10.1038/s41588-024-01937-x](https://doi.org/10.1038/s41588-024-01937-x) ::: {.callout-important} For scores from the PGS Catalog, please remember to cite the original publications from which they came (these are listed in the metadata table). diff --git a/docs/explanation/match.rst b/docs/explanation/match.rst index 85449b4c..3bcdb131 100644 --- a/docs/explanation/match.rst +++ b/docs/explanation/match.rst @@ -22,7 +22,7 @@ What is matching? The calculator carefully checks that variants (rows) in a scoring file are present in your target genomes. -The matching procedure `is described in the preprint supplement `_. +The matching procedure `is described in supplement of our recent publication `_. The matching procedure never makes any changes to target genome data and only seeks to match variants in the scoring file to the genome. diff --git a/docs/index.rst b/docs/index.rst index 96863956..1d9932ea 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -164,13 +164,13 @@ Citations If you use ``pgscatalog/pgsc_calc`` in your analysis, please cite: - Lambert, Wingfield, `et al.` (2024) The Polygenic Score Catalog: new functionality and tools to enable FAIR research. medRxiv. doi:`10.1101/2024.05.29.24307783`_. + Lambert, Wingfield, `et al.` (2024) Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization. Nature Genetics. doi:`10.1038/s41588-024-01937-x`_. In addition, please remember to cite the primary publications for any PGS Catalog scores you use in your analyses, and the underlying data/software tools described in the `citations file`_. .. _citations file: https://github.com/PGScatalog/pgsc_calc/blob/master/CITATIONS.md -.. _10.1101/2024.05.29.24307783: https://doi.org/10.1101/2024.05.29.24307783 +.. _10.1038/s41588-024-01937-x: https://doi.org/10.1038/s41588-024-01937-x License Information