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Develop 3.9.0#417

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kathy-nevola merged 63 commits intomainOlink-Proteomics/OlinkRPackage:mainfrom developOlink-Proteomics/OlinkRPackage:developCopy head branch name to clipboardAug 6, 2024

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Commits on Jun 20, 2024

• LOD both methods additions

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• shrink logo

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Commits on Jun 21, 2024

• Merge remote-tracking branch 'origin/lod_updates' into lod_both_methods

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• Add both section to tutorial

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• Merge remote-tracking branch 'origin/lod_updates' into lod_both_methods

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• add documentation on both methods

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Commits on Jul 11, 2024

• updated tutorial links

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• Add instructions for multiple NPX file import in Vignett.html

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• Added additional information about LOD from counts

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Commits on Jul 12, 2024

• ignore quote for comma delim

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• add new headers and remove QC_Warning as required

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• Add quant warning

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• update file to remove rowname and quotes

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• Merge branch 'develop' into lod_both_methods

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Commits on Jul 17, 2024

• Update instructions to write parquet file

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• Add HT Bridging sample recommendations

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Commits on Jul 19, 2024

• Add missing link and search terms

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• Merge pull request #402 from Olink-Proteomics/new_links

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• Merge pull request #409 from Olink-Proteomics/HT_bridge_samples

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Commits on Jul 22, 2024

• Merge branch 'develop' into write_parquet

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• Update Description, News and Cran comments

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• spelling fix

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• reworded for clarity

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• Merge pull request #408 from Olink-Proteomics/write_parquet

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• Merge pull request #406 from Olink-Proteomics/csv_added_support

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Commits on Jul 24, 2024

• Merge branch 'develop' into lod_both_methods

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• Merge branch 'develop' into LOD_count_info

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• Add an error in ANOVA functions when control assays have not been removed.

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• Update OlinkAnalyze/vignettes/Vignett.Rmd

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• Update OlinkAnalyze/vignettes/Vignett.Rmd

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Commits on Jul 25, 2024

• Merge pull request #403 from Olink-Proteomics/develop_dgt

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• updated with recommended changes from review

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• Merge pull request #404 from Olink-Proteomics/LOD_count_info

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• fix bullet points in documentation

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• fixed table and wording per review

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• added documentation and checks for file

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• added ANOVA error update

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• Apply suggestions from code review

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Commits on Jul 26, 2024

• Merge pull request #390 from Olink-Proteomics/lod_both_methods

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Commits on Jul 29, 2024

• Change if statement for assay type, add list of found control assays to error message

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Commits on Jul 30, 2024

• Add error in Olink ANOVA functions when external controls are present. Add unit tests for this error. Update Olink_anova.R and Vignett.Rmd with documentation instructing users to remove internal an…

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• Document

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• fix example documentation and make ctrl in name warning

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• added control samples warning/error

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Commits on Jul 31, 2024

• remove ctrl sample check code and tests

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• update documentation

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• Remove unnecessary tests

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• update news per PR #416

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• remove sample test DF

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• update vignette

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• update vignette boxplot

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• updated vignette posthoc

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• Merge pull request #416 from Olink-Proteomics/OA-2272_trycatch_controls

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• Merge pull request #415 from Olink-Proteomics/news_3.9

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Commits on Aug 2, 2024

• change to new pipe

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• remove scale_name (now name)

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• remove name arguement

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• fix dot notation and remove deprecated do statement

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• fix internal function documentation

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Commits on Aug 5, 2024

• added scale_name as deprecated for support with older ggplot2 versions

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• update scale name to work with ggplot per version

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Commits on Aug 6, 2024

• Merge pull request #421 from Olink-Proteomics/anova_pipes

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• spelling edit fixes

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