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Olink Analyze 3.7.0
Minor Changes
- Support for Explore 3072 data in parquet form added (#327, @kathy-nevola, @klevdiamanti)
- Support for pathway enrichment when LOD is not present added (#329, @kathy-nevola)
- Clarification to remove controls when selecting bridging samples added in bridging tutorial (#330, @kathy-nevola)
- Addition of Kristyn Chin as contributor (#331, @kathy-nevola)
- Addition of URLs and Contact information in Description (#331, @kathy-nevola)
Olink Analyze 3.6.2
Bug Fixes
- Packages in Suggest field are now called conditionally in vignettes, tests, and examples. (#319, @kathy-nevola)
- read_NPX will now work with Target 96 data that does not contain “Target 96” in the panel name (#320, @kathy-nevola)
- olink_lmer will no longer require the presence of an Index column in the data (#321, @kathy-nevola)
- corrected examples for subset normalization (#312 @kathy-nevola)
- added additional information on example data to outlier vignette (#313 @kathy-nevola)
- clarified documentation for longitudinal randomization (#314 @kathy-nevola)
- corrected warning message for olink_ordinalRegression (#296 @boxizhang)
Olink Analyze 3.6.1
Minor Changes
- Install package Matrix from source in CI. (#299 @klevdiamanti, @AskPascal)
Olink Analyze 3.6.0
Minor Changes
- Plate LOD will be chosen over Max LOD when both are present (#288, @kathy-nevola)
- Data from NPX Signature 1.8+ is now supported by read_NPX when in long format csv (#293, @Orbmac, @kathy-nevola)
- olink_pca_plot will now be faster (#289, @MasoumehSheikh)
Bug Fixes
- olink_normalization and related function will now compare normalization strategy by assay (#291, klevdiamanti)
- Excluded assays will not cause warnings in olink_normalization (#291, klevdiamanti)
- olink_pca_plot will now show the same label and text for point when SampleID is numeric (#289, @MasoumehSheikh)
Olink Analyze 3.5.1
Bug Fixes
- read_NPX will now support additional formats of parquet files
Olink Analyze 3.5.0
Minor Changes
- read_NPX will now detect and import Flex excel files in wide format (@kathy-nevola, #234)
- Add example of bridge samples selector and minor updates for clarity to Intro to bridging vignette (@Orbmac, @kathy-nevola, #260)
- Increase plate randomizer unit test coverage (@amrita-kar, #264)
- Add support for parquet files in read_NPX (@kathy-nevola, #265, @klevdiamanti, #270)
- Add support for alternative forms of LOD including Max and Plate LOD (@kathy-nevola, #267)
- Add support for SampleQC column (alternative to QC_Warning) (@kathy-nevola, #267, @MasoumehSheikhi, @268)
- Add support for plate randomization with variable control numbers (@kathy-nevola, @AskPascal, #269)
- Controls can now be randomized across the plate with olink_plate_randomizer (@kathy-nevola, @AskPascal, #269)
- Minor updates for clarity to Plate Randomization vignette (@kathy-nevola, @AskPascal, #269)
- Change formatting for long format Target CSVs to match excel (@kathy-nevola, #273)
Bug Fixes
- Project name is now consistent and generic throughout bridging vignette (@kathy-nevola, #257)
- Estimate is now included in output when Paired Mann-Whitney U test is performed (@boxizhang, #259)
Olink Analyze 3.4.1
Bug Fixes
- Skip PCA snapshot tests in R version > 4.2.3 (@AskPascal, #254)
- Bridge selector will now return all samples when requesting max number of samples based on missing frequency (@klevdiamanti, #252)
- Fixed unit tests to expect NA as logical instead of “NA” as character (@MasoumehSheikhi, #250)
Olink Analyze 3.4.0
Minor Changes
- User can now specify label for proteins in olink_heatmap_plot() (@simfor, #228)
- Updates to unit test and CI based on dependency changes (@AskPascal, #231, #236, #240)
- Addition of normalization functions to simplify bridge, subset, and multi-batch normalization (@klevdiamanti, #201)
- Introduction to bridging vignette added (@leiliuC, @kathy-nevola, #174)
- Plate Randomization vignette added (@boxizhang, #241)
- Outlier Exclusion vignette added (@kathy-nevola, #229)
- Added Lei Conze as author (@kathy-nevola, #246)
- Addition of citation (@kathy-nevola, #246)
Bug Fixes
- Update to olink_wilcox documentation and UniProt description in documentation has been corrected (@boxizhang, #235)
Olink Analyze 3.3.1
Bug Fixes
- olink_pathway_enrichment now prints a message when there are non matching names when using method = “ORA” (@MasoumehSheikhi, #222)
- olink_pca_plot will now generate PCA when data is missing from the first OlinkID (@kathy-nevola, #221)
- read_NPX now supports csv files with Sample_Type column but not ExploreVersion column (@klevdiamanti, #220)
- extra columns in input file will no longer result in a warning message (@kathy-nevola, #223)
Olink Analyze 3.3.0
Minor Changes
- Support for additional versions of Olink data - Read_NPX now supports a wider range of Olink data types (@AskPascal, @kathy-nevola, #207, #208, #211, #216)
- Automatic support for normalizing 2 datasets with different column configurations - olink_normalization will now automatically add missing columns to datasets (filled NA) to allow data with different configurations to be more easily normalized together (@kathy-nevola, #212)
- Automatic checking that datasets used the same normalization method before bridging - Datasets that were normalized with different methods (different values in normalization column) will now warn before performing normalization (@klevdiamanti, #210)
Bug Fixes
- Data with ‘#’ in SampleID column is now supported (@AskPascal, #208)
- PCA can now be generated when indices are not consistent across SampleIDs (@amrita-kar, #206)
Olink Analyze 3.2.2
Bug Fixes
- remove www. from links in vignette to prevent rerouting of URL (@kathy-nevola, #188)
- update set_plot_theme() to use linewidth instead of size per ggplot2 3.4
Olink Analyze 3.2.1
Bug Fixes
- Change in unit test to write to temporary directory (@AskPascal, #181)
Olink Analyze 3.2.0
Minor Changes
- Addition of functions to perform Uniform Manifold Approximation and Projection (UMAP) dimensional reduction and plots (@simfor, #139)
- Add additional install methods to Readme (@AskPascal, #153)
- ggrepel can now be disabled when outlier lines are present in the PCA plot (@klevdiamanti, #158)
- Long running unit tests are now skipped on CRAN (@AskPascal, #163)
- Internal functions were added to read_NPX to support future development (@klevdiamanti, #167)
- CI workflows were refactored to utilize external actions (@AskPascal, #169)
- Read_NPX will now warn the user when NAs are detected in the NPX column (@AskPascal, #170)
- Friedman test interface and documentation was updated to be more intuitive (@boxizhang, #171)
Bug fixes
- Pathway enrichment p-values are now in the correct order when plotting (@klevdiamanti, #164)
- PCAs now behave the same with any locale (@AskPascal, #173)
- Read_NPX now accepts either Panel_Version or Panel_Lot_Nr in input files (@klevdiamanti, #156)
- Assays that only have NPX = NA will now be excluded from all analyses and figures (@simfor, @kathy-nevola, @AskPascal, #176)
- Refactor code to use tidyselect::all_of() in recommended way (@AskPascal, #177)
- vdiffr based unit tests were reactivated (@AskPascal, #172)
Olink Analyze 3.1.0
Minor Changes
- Non-parametric functions are now available (@boxizhang, #114, #142)
- Updated installation instructions to reflect CRAN acceptance (@kathy-nevola, #107)
- Zipped files from MyData can now be used as input for read_NPX (@klevdiamanti, #115)
- LME and ANOVA formulas can now be customized (@jrguess, #120)
- Pathway enrichment functions and visualizations are now available (@kathy-nevola, #125)
- Heatmaps can now be generated (@Orbmac, $127)
- olink_boxplot function now has significance bars and stars (@boxizhang, #132)
- PCA preprocessing was moved to internal function (@simfor, #133)
- olink_plate_randomizer will now return a warning if there are duplicate SampleIDs or if SubjectColumn is missing (@kristianHoden, #146)
- olink_plate_randomizer can now keep studies together on plates (@kristianHoden, #146)
- Added Masoumeh Sheikhi and Boxi Zhang as authors
- Added Kristian Hodén as contributor
Bug Fixes
- olink_pca_plot by Panel will now show correct colors when a variable is missing (@MasoumehSheikhi, Issue #117, Commit 0f2f157)
- olink_ttest will now return a warning message if an assay has less than 2 datapoints in a group. (@marisand, #110)
- LMER class is now checked using inherits (@MasoumehSheikhi, #134)
- License was corrected to AGPL-3 (@Orbmac, #138)
- Correct output type of olink_dist_plot in vignette to ggplot object (@kathy-nevola, Issue #112, #141)
- Previously called “intensity normalization” has been clarified as a special type of subset normalization and an example has been added to the documentation and vignette (@Orbmac, #144)
Olink Analyze 3.0.0
Major Changes
- displayPlateDistributions and displayPlateLayout names were updated to olink_displayPlateDistributions and olink_displayPlateLayout (@simfor, #98)
Minor Changes
- Update CI to Ubuntu 20.04 (@AskPascal, #97)
- olink_bridgeselector will now give an error if less than n (number of) bridge samples can be selected based on set sampleMissingFreq (@marisand, #100)
- update return value documentation for all functions to specify columns and class of output (@kathy-nevola, #102)
- replaced or removed cat/print with message/stop so messages printed to the console can be suppressed (@jrguess, #103)
Bugfixes
- fixed spelling mistakes in documentation (@kathy-nevola, #92)
- updated DESCRIPTION to fit CRAN specification (@kathy-nevola, #94)
- change T/F to TRUE/FALSE for stability (@AskPascal, #96)
- updated documentation to olink_plate_randomizer, olink_displayPlateDistributions and olink_displayPlateLayout to link related functions and clarify olink_plate_randomizer documentation (@simfor, #98)
- fixed keywords in documentation (@kathy-nevola, #99)
Olink Analyze 2.0.1
Bug Fixes
- Remove hexagon from Readme (@kathy-nevola, #86)
- Replace OlinkAnalyze with Olink® Analyze (@kathy-nevola, #86)
- Add Ola Caster to author list
- Update documentation to change olinkR to Olink Analyze (@jrguess, #89)
Olink Analyze 2.0.0
Major Changes
- Package is in the process of being submitted to CRAN
- Added ability to prevent OlinkAnalyze from loading fonts and setting to themes (@OlaCaster, #73)
- Decreased the size of npx_data1 and npx_data2 to 2 panels instead of 12 (@kathy-nevola, #76)
- Updates to the olink_qc_plot and olink_pca_plot functions (@simfor, #78)
BugFixes
- Moved NEWS.md to correct level (@kathy-nevola, #74)
- Added cran-comments.md file to document Notes for CRAN submission (@kathy-nevola, #74)
- Update Vignette to reflect new functionality (@kathy-nevola, #78)
Olink Analyze 1.3.0
Major Changes
- DESCRIPTION file updated to include all authors and maintainers (@kathy-nevola, #66)
- Unit testing was added (@marisand, @simfor, #65, #55, #47)
- Continuous Integration (CI) was added (@AskPascal, #57, #53, #40, #31)
read_NPX now converts Panel Names to Sentence case except Roman Numerals (@kathy-nevola, #44)- Output order of
olink_bridgeselector() is now randomized (@marisand, #60)
- PlateSize argument was added to
displayPlateLayout() and olink_plate_randomizer for T48 and T96. Hardcoded sizes have been removed. (@marisand, #47)
- Changed
olink_pal() to have gray instead of light blue (@marisand, #22)
Bug Fixes
set_plot_theme() will now load Swedish Gothic Thin if available on all OS (@marisand, @AskPascal, #70, #39)- Help documentation was updated to correct typos and clarify notation for ANOVA and LME models (@kathy-nevola, @marisand,@AskPascal #67, #33, #37)
- Fix
olink_dist_plot() from showing multiple bars when sample has QC warning in some assays (@marisand, @AskPascal, #64)
- Fix
olink_qc_plot() from showing multiple points/labels when sample has QC warning in some assays (@marisand, @AskPascal, #63)
- Panel names in npx_data1 and npx_data2 were fixed to match new
read_NPX() formatting (@kathy-nevola, #62)
olink_bridgeselector() QC warning filtering changed to match olink_qc_plot() and olink_dist_plot() (@marisand, @AskPascal, #61)- global variables are now specified (@kathy-nevola, #45)
- Function documentation updated to remove notes on R CMD check (@kathy-nevola, #39)
- Fix summary casting “tukey” to “sidak” adjustment warning in
olink_anova_posthoc() and olink_lmer_posthoc() functions (@marisand, #38)
- Update functions to import selectively (@kathy-nevola, @Orbmac, @AskPascal, @marisand, #21, #20, #19, #18, #15, #29)
- Fix guides size argument in
olink_pca_plot() (#17) (@AskPascal, #24)
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