read_npx() (@klevdiamanti)read_npx() (and its alias read_NPX()) has
been fully rewritten with improved architecture, splitting the
monolithic reader into dedicated sub-readers for each file format:
Excel, delimited (CSV/TSV), Parquet, ZIP archives, and wide-format qPCR
exportsout_df (output format), long_format,
olink_platform, data_type,
.ignore_files, quiet, and
legacy.check_npx() function (@klevdiamanti, @MasoumehSheikhi & @KangD-dev)check_npx() validates NPX data
for correctness and completeness before downstream analysis.clean_npx().check_npx() is now used
in all the functions in downstream analysis to allow for alternative
column names and provide consistent and informative warnings and errors
when data issues are detected.clean_npx() function (@klevdiamanti & @KangD-dev)clean_npx() applies an
automated quality-control cleaning pipeline to remove unsuitable data
records.read_NPX(), have been renamed
to their equivalent snake case read_npx() to be more
intuitive and consistent with R naming conventions. Previous function
names are retained as aliases for backward compatibility.arrow, duckdb, and dbplyr are
now imported for enhanced Parquet file support and efficient data
processing.cli is now used for most user-facing messages,
warnings, and error reportingmagrittr pipe (%>%) has been
replaced by the native R pipe (|>). throughout the
package; magrittr is no longer a dependency.olink_osi_dist_plot() function has been added for
visualizing Olink Sample Index (OSI) values distributions.olink_qc_plot(),
olink_pca_plot() and olink_umap_plot() now
have full support for OSI values.testthat edition 3, and test coverage extended
to >90%.broom, car, emmeans,
ggpubr, ggrepel, readxl,
rstatix, FSA) to reduce the package’s
installation footprintolink_wilcox() are now arranged by Assay name
to handle ties (#616, @boxizhang)extrafont package has been removed as a dependency
as it is archived on CRAN (#619, @klevdiamanti)olink_lmer() has been improved to better
capture the warning message (#618, @klevdiamanti)AssayQC is not present in both data
sets for normalization (#620, @klevdiamanti)olink_lod() call to checkNPX() now
correctly uses data instead of df, allowing the function to run without
error (#579, @klevdiamanti)olink_bridgeselector() to clarify how to set
sampleMissingFreq argument for different products and
biological contexts (#597, @amrita-kar, #596, @kathy-nevola)read_NPX now converts Panel Names to Sentence case
except Roman Numerals (@kathy-nevola, #44)olink_bridgeselector() is now
randomized (@marisand, #60)displayPlateLayout()
and olink_plate_randomizer for T48 and T96. Hardcoded sizes
have been removed. (@marisand, #47)olink_pal() to have gray instead of light blue
(@marisand,
#22)set_plot_theme() will now load Swedish Gothic Thin if
available on all OS (@marisand, @AskPascal, #70, #39)olink_dist_plot() from showing multiple bars when
sample has QC warning in some assays (@marisand, @AskPascal, #64)olink_qc_plot() from showing multiple points/labels
when sample has QC warning in some assays (@marisand, @AskPascal, #63)read_NPX() formatting (@kathy-nevola, #62)olink_bridgeselector() QC warning filtering changed to
match olink_qc_plot() and olink_dist_plot()
(@marisand, @AskPascal, #61)olink_anova_posthoc() and olink_lmer_posthoc()
functions (@marisand, #38)olink_pca_plot() (#17)
(@AskPascal,
#24)
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