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Develop#494

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kathy-nevola merged 170 commits intomainOlink-Proteomics/OlinkRPackage:mainfrom developOlink-Proteomics/OlinkRPackage:developCopy head branch name to clipboardJan 27, 2025

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Commits

Commits on Oct 1, 2024

• Update minimum number of bridge samples for HT-3k

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• Merge pull request #466 from Olink-Proteomics/develop

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Commits on Oct 15, 2024

• convert block to char when read from CSV

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Commits on Oct 30, 2024

• New function to plot bridgeable assays

  

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• Fixed the issue of repaeating assays in a loop so now each assay is on a page

  

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Commits on Nov 4, 2024

• Removed dependency on new packages and just used ggplot2 and ggpubr packages in the code. Also added function documentation

  

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• Document

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• Updated donttest case and man pages for the function. Also ran the devtools checks.

  

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Commits on Nov 5, 2024

• Updated man pages and ran devtools check locally.

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• Updated the man pages and variable naming to pass devtools checks.

  

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Commits on Nov 6, 2024

• Test update

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• test

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• Fixed some check errors and filters for minimum counts in R2 plots.

  

  Amrita Kar

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• remove default setting for data, changed Panel to Project, added check for Project, fixed spacing for example

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• Merge pull request #470 from Olink-Proteomics/fix_plots

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• Merged results from fix plots and fixed linting issues.

  

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Commits on Nov 7, 2024

• Fixed plot layout and color on text label for bridgeable (green) and non-bridgeable assays (red).

  

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Commits on Nov 8, 2024

• Updating read_NPX and normalization sections

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• Shortening t-test, ANOVA, LME sections

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Commits on Nov 12, 2024

• Add initial function and tests for formatting of olink_normalization_product output

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Commits on Nov 13, 2024

• Remove control samples and concatenate SampleID and Project when olink_normalization_product_format is run. Add argument to olink_normalization to toggle whether formatting is applied.

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• Edit function description

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• Document

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• Fix function description

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• Merge branch 'develop_product_bridging_downstream' of github.com:Olink-Proteomics/OlinkRPackage into develop_product_bridging_downstream

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Commits on Nov 14, 2024

• Simplifying vignette text in stats & vis sections

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Commits on Nov 15, 2024

• update documentation

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Commits on Nov 16, 2024

• Added standardized colors to bridgeable and non-bridgeable assays. Also added a median of negative controls for approximate LOD in the correlation plot.

  

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Commits on Nov 18, 2024

• Update OlinkAnalyze/vignettes/Vignett.Rmd

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• Update OlinkAnalyze/vignettes/Vignett.Rmd

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• Update OlinkAnalyze/vignettes/Vignett.Rmd

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Commits on Nov 19, 2024

• Merge branch 'vignette_updates_KC' of https://github.com/Olink-Proteomics/OlinkRPackage into vignette_updates_KC

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• Merge branch 'develop' of github.com:Olink-Proteomics/OlinkRPackage into develop_product_bridging_downstream

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• Generate lower res images for vignette

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• Merge branch 'develop' into vignette_updates_KC

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• Revert "Merge branch 'develop' into vignette_updates_KC"

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• Remove extra plot saved in main folder

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Commits on Nov 21, 2024

• Removed negative controls from R2 and added captions for R2 plots

  

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• bug fix for fredman posthoc

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• Document

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Commits on Nov 22, 2024

• Update Vignett.Rmd

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• Merge branch 'develop' of https://github.com/Olink-Proteomics/OlinkRPackage into vignette_updates_KC

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• update token to OA_PAT

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Commits on Nov 25, 2024

• update study documentation and tutorial

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• add back library call

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• Merge branch 'develop' into develop_3k-HT_plots

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• Merge branch 'develop' into OA-478

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• Merge branch 'develop' into block_as_char

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• Merge pull request #465 from Olink-Proteomics/develop_3k-HT_num_samples

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Commits on Nov 29, 2024

• Merge pull request #474 from Olink-Proteomics/block_as_char

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• Fix internal control error in olink_anova to not trigger for the CTRL protein assay.

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Commits on Dec 2, 2024

• bug fix for fredman posthoc

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Commits on Dec 5, 2024

• Made edits per review

  

  Amrita Kar

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• Merge branch 'develop_3k-HT_plots' of github.com:Olink-Proteomics/OlinkRPackage into develop_3k-HT_plots

  

  Amrita Kar

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• Commented on linting issues. Added seed for the KS test and changed KS test input to be consistent with the olink_normalization_bridgeable()

  

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• Merge pull request #468 from Olink-Proteomics/develop_3k-HT_plots

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Commits on Dec 6, 2024

• Add new unit test to confirm no error is thrown when CTRL assay present. Change anova and posthoc variable to "treatment2" for some tests, as the "Site" column is not present.

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Commits on Dec 16, 2024

• Adding documentation to general vignette for olink_normalization_product_format, bridgeable_plts

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• Pulling previous changes

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• Addressing conflicts in bridgeable_plts section

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• Delee duplicate vignette

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Commits on Dec 17, 2024

• Merge pull request #483 from Olink-Proteomics/OA-2168_randomization_study

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Commits on Dec 18, 2024

• Update olink_normalization_product_format to include NotBridgeable and NotOverlapping assays with their original OlinkIDs and NPX values.

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• Merge branch 'develop' of github.com:Olink-Proteomics/OlinkRPackage into develop_product_bridging_downstream

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Commits on Jan 7, 2025

• add reveal support

  kathy-nevola

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• add reveal support, change error to warning for metadata

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• add reveal

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Commits on Jan 13, 2025

• upgrade set to TRUE to fix fgsea error on CI

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• remove upgrade, add fgsea as additional package

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• specify to install fgsea from bioconductor

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Commits on Jan 14, 2025

• add separate step to install fgsea

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• hardcode bioc version as remotes is not using newest version

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• fix syntax

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• fix syntax

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• revert and remove cache

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• remove NPX Explore ref for generalized Olink SW

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• Update to contact us and legal disclaimer

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• add logo to tutorials

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Commits on Jan 15, 2025

• A test

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• Dont set BioC version

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• Do not update Ubuntu libraries

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• Cache R dependencies

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• Remove BioC installation step from render-and-document

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• Remove BioC installation from remotes

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• Add back OSX and Windows in R-CMD-check

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• Test on Ubuntu 20.04, Ubuntu 22.04, Windows and OSX

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• Swap Ubuntu 22.04 R devel to Ubuntu 24.04

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• R devel CI runs on Ubuntu 24.04

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• R-CMD-docker R 4.4.0 -> 4.4.2

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• Workflow on OSX runs on pull_request

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• Workflow on Ubuntu 22.04 runs on pull_request

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• Workflow for Windows runs on pull_request

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• Workflow for Ubuntu 20.04 runs on pull_request

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• Workflow on Ubuntu 24.04 R devel runs on pull_request

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• Remove step that updates Ubuntu libraries

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• Allow caching of R dependencies

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• Merge pull request #489 from Olink-Proteomics/fgsea-ci-fix-kd

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• Merge pull request #488 from Olink-Proteomics/fgsea_ci_fix

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Commits on Jan 16, 2025

• Added RUO message per OA2318

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Commits on Jan 21, 2025

• Fix bug to allow HT-HT bridge normalization.

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• Test that HT-HT bridging works.

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• Merge pull request #484 from Olink-Proteomics/anova_ctrl_fix

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• Merge pull request #491 from Olink-Proteomics/develop_ht-to-ht_brdging

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Commits on Jan 22, 2025

• update based on the feedback for fredman posthoc

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• update based on the feedback for fredman posthoc

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• update based on the feedback for fredman posthoc

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• update based on the feedback for fredman posthoc

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• Rename to fix linting

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• Update check and cli message for product

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• Add withr to suggested packages

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• Improved RUO message

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• Test for RUO parquet file

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• Improved cli warning for DataFileType

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• Switch to cli::cli_abort

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• New R pipe

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• Update tests for RUO parquet files

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• skip_if_not_installed does not accept vectors

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• Typo correction in vignette

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• Adding contact information and legal disclaimer

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• Updated copyright statements

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• Merge pull request #490 from Olink-Proteomics/copyright_name

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• remove unnecessary check of columns

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Commits on Jan 23, 2025

• Harmonizing language in vignette

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• Merge branch 'develop' into vignette_updates_KC

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• Update get_example_data function and calls with new file location

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• Move cross-product bridging formatting doc to 3K-HT vignette

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• Merge with develop branch

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• Resolving conflicts in legal statement

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• Fixing typo in coding examples

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• Incorporating feedback

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• fix test example data interaction

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• added missing selective call for dpylr stars_with

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Commits on Jan 24, 2025

• Merge pull request #487 from Olink-Proteomics/reveal

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• Fix dplyr package call and confirm devtools::checks() pass

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• update Description and news

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• remove excess new lines

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• Rename bridgeability plot func, add to 3K-HT vignette

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• Changed name from bridgeable_plot to olink_bridgeability_plot based on poll

  

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• Document

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• Harmonize code samples & remove NAs from boxplots

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• Merge pull request #473 from Olink-Proteomics/vignette_updates_KC

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• Order output by Project and SampleID

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• renamed bridgeability plot

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• Merge pull request #472 from Olink-Proteomics/develop_product_bridging_downstream

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• Merge pull request #493 from Olink-Proteomics/rename_function

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• Replace tab with space

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• review comment updates

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• Update OlinkAnalyze/NEWS.md

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• Merge pull request #492 from Olink-Proteomics/news_4.1.0

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• Merge branch 'OA-478' of https://github.com/Olink-Proteomics/OlinkRPackage into OA-478

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• Merge branch 'develop' into OA-478

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• Update News

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• Revert "Vignette Updates - Simplifying Existing Vignette"

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• pull updates to tutorials into reverted branch

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• update order of OlinkID on product test

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• Merge pull request #496 from Olink-Proteomics/revert-473-vignette_updates_KC

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• Merge pull request #497 from Olink-Proteomics/fix_dev

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• Merge branch 'develop' into OA-478

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• remove old version of bridgeability function

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• Merge pull request #485 from Olink-Proteomics/OA-478

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• add missing parameter

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• remove print statment

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• update select statement to use any_of instead of vector

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• change vector to any_of

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• fix spelling

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• add back missing figures from tutorial

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• Merge pull request #498 from Olink-Proteomics/fix_dev2

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Commits on Jan 27, 2025

• adjusted links to remove www

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• fix keyword formatting in documentation

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• Merge pull request #499 from Olink-Proteomics/fix_dev2

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