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gDRutils 1.11.14 - 2026-09-21
move the response threshold that decides the constant-fit xc50 sign from code into the fit_config block, keyed by normalization type
ensure the fit configuration is read when the fitting layer is entered directly rather than through apply_fit()
gDRutils 1.11.13 - 2026-09-21
move per-normalization-type fit configuration from code into fit_profiles.json
gDRutils 1.11.12 - 2026-09-19
move the generic fitting layer here from gDRcore: apply_fit() , apply_fits() , apply_fit_to_se() , the fit profile registry and the reference fit function
add persist_fit_assay() for writing fit results into a BumpyMatrix assay, shaped over the full SE dimensions and raising an error for row or column names the SE does not have
fix the package becoming unloadable where the fit profile file does not resolve, by reading the profiles on first use instead of during package load
gDRutils 1.11.11 - 2026-09-11
set missing fit_source to “gDR” when merging assays so merged data keeps all cell lines
gDRutils 1.11.10 - 2026-08-17
remove alignment whitespace flagged by the gDRstyle linter
document internal helper functions with @keywords internal
gDRutils 1.11.9 - 2026-08-10
convert BumpyMatrix factor columns to character in convert_se_assay_to_dt
gDRutils 1.11.8 - 2026-07-29
fix split_SE_components to return empty list instead of empty data.frame when no constant columns exist
gDRutils 1.11.7 - 2026-07-28
fix get_gDR_session_info to compare versions numerically, avoiding false “outdated” warnings (e.g. 0.2.100 vs 0.2.99)
gDRutils 1.11.6 - 2026-07-20
remove redundant split_SE_components calls
gDRutils 1.11.5 - 2026-07-01
improve average_biological_replicates_dt performance with GForce-friendly operations
gDRutils 1.11.4 - 2026-06-11
improve curve fitting performance
gDRutils 1.11.3 - 2026-05-27
apply updated gDRstyle rules
gDRutils 1.11.2 - 2026-05-05
update author email address
gDRutils 1.11.1 - 2026-04-29
synchronize Bioconductor and GitHub versioning
gDRutils 1.9.8 - 2026-04-18
migrate from qs to qs2 package (qs::qread → qs2::qs_read , qs::qsave → qs2::qs_save )
update batch file extension from .qs to .qs2
gDRutils 1.9.7 - 2026-04-14
add support for metadata in merge_MAE
gDRutils 1.9.6 - 2026-03-23
standardize_MAE standardizes also internal identifiers
gDRutils 1.9.5 - 2026-02-12
remove_drug_batch supports atomic vectors as input
gDRutils 1.9.4 - 2025-12-02
convert_se_assay_to_dt supports merging additional variables
gDRutils 1.9.3 - 2025-11-27
add support for the time-course experiment
gDRutils 1.9.2 - 2025-11-03
update merge_SE function to merge drugs with different batches together
gDRutils 1.9.1 - 2025-10-30
synchronize Bioconductor and GitHub versioning
gDRutils 1.7.18 - 2025-09-30
add predict_smooth_from_combo function
gDRutils 1.7.17 - 2025-08-12
gDRutils 1.7.16 - 2025-08-05
fix convert_se_assay_to_dt to display appropriate columns
add flag for capping values in convert_se_assay_to_custom_dt
gDRutils 1.7.15 - 2025-08-01
improve logic in split_SE_components
gDRutils 1.7.14 - 2025-07-28
replace row/col_fittings in source for matrix Metrics assay
gDRutils 1.7.13 - 2025-07-14
add “maxlog10Concentration” and “N_conc” to headers list
gDRutils 1.7.12 - 2025-07-01
refactor average_biological_replicates_dt to properly average data
gDRutils 1.7.11 - 2025-06-24
add support in merge_MAE for merging mixed experiments
gDRutils 1.7.10 - 2025-06-09
update loop to support batch approach
gDRutils 1.7.9 - 2025-06-04
gDRutils 1.7.8 - 2025-05-26
gDRutils 1.7.7 - 2025-05-21
add support for combo data in merge_SE
add merge_MAE fun
gDRutils 1.7.6 - 2025-05-13
add append arg to .set_SE_metadata
gDRutils 1.7.5 - 2025-05-12
improve logic in cap_assay_infinities
gDRutils 1.7.4 - 2025-05-07
update cap_assay_infinities
add additional grouping columns in cap_assay_infinities
gDRutils 1.7.3 - 2025-04-28
add result entries in headers_list for combination data
gDRutils 1.7.2 - 2025-04-17
refactor get_gDR_session_info to display used packages
gDRutils 1.7.1 - 2025-04-16
synchronize Bioconductor and GitHub versioning
gDRutils 1.5.17 - 2025-03-26
fix default parameter in get_settings_from_json
gDRutils 1.5.16 - 2025-03-19
add get_gDR_session_info function
gDRutils 1.5.15 - 2025-03-18
move split_big_table_for_xlsx from gDRsearch2 package
gDRutils 1.5.14 - 2025-03-12
improve logic in get_assay_req_uniq_cols
gDRutils 1.5.13 - 2025-03-07
add support for combination experiment in cap_assay_infinities
move map_conc_to_standardized_conc from gDRcore package
gDRutils 1.5.12 - 2025-02-21
refactor average_biological_replicates
gDRutils 1.5.11 - 2025-02-14
update default value of capping_fold param in cap_assay_infinities
gDRutils 1.5.10 - 2025-02-05
add support for dropping masked values in the assay data
gDRutils 1.5.9 - 2025-02-03
keep ‘replicate’ column as additional perturbation in get_additional_variables
gDRutils 1.5.8 - 2025-01-30
add support for unifying metadata in convert_se_assay_to_dt function
gDRutils 1.5.7 - 2025-01-24
gDRutils 1.5.6 - 2025-01-13
refactor remove_drug_batch
gDRutils 1.5.5 - 2024-12-10
make split_SE_components working correctly for sa assay data, modified with avearge_biological_duplicates
gDRutils 1.5.4 - 2024-12-09
improve in the logic of average_biological_replicates (new blacklisted column)
gDRutils 1.5.3 - 2024-12-02
refactor set_unique_* functions
gDRutils 1.5.2 - 2024-11-05
gDRutils 1.5.1 - 2024-11-05
synchronize Bioconductor and GitHub versioning
gDRutils 1.3.17 - 2024-10-24
make average_biological_replicates_dt more restrictive - fewer columns to check for duplicates
gDRutils 1.3.16 - 2024-10-11
make duplicates’ helpers supporting combo assays as well
gDRutils 1.3.15 - 2024-10-07
refactor the logic for dealing with duplicates in assay data
gDRutils 1.3.14 - 2024-10-03
fixed issue in average_biological_replicated (fit_type)
gDRutils 1.3.13 - 2024-09-16
add functions set_unique_cl_names_dt and set_unique_drug_names_dt
gDRutils 1.3.12 - 2024-09-04
remove hack with checkDimnames
gDRutils 1.3.11 - 2024-08-30
remove GDS fit_source from gDRviz
gDRutils 1.3.10 - 2024-08-28
extend the logic of get_additional_variables to support other sources of fitting metrics
gDRutils 1.3.9 - 2024-08-14
extend the logic of average_biological_replicates_dt to calculate standard deviation
gDRutils 1.3.8 - 2024-08-06
add functions for setting unique identifiers in the colData and rowData of SE
gDRutils 1.3.7 - 2024-07-30
refactor average_biological_replicates_dt and get_additional_variables to support unprettified identifiers
gDRutils 1.3.6 - 2024-07-17
update define_matrix_grid_positions
gDRutils 1.3.5 - 2024-07-12
move get_combo_col_settings and get_iso_colors to gDRplots package
gDRutils 1.3.4 - 2024-07-08
add residual sum of square and p-value to Metrics assay
gDRutils 1.3.3 - 2024-07-03
add vignette section about prettifying logic
gDRutils 1.3.2 - 2024-06-24
gDRutils 1.3.1 - 2024-05-27
synchronize Bioconductor and GitHub versioning
gDRutils 1.1.17 - 2024-05-22
gDRutils 1.1.16 - 2024-05-22
move convert_se_assay_to_custom_dt, capVals and get_settings_from_json from gDRcomponents package
gDRutils 1.1.15 - 2024-05-17
simplify logic of supported experiments
gDRutils 1.1.14 - 2024-05-16
move define_matrix_grid_positions and round_concentration functions from gDRcore package
gDRutils 1.1.13 - 2024-05-08
gDRutils 1.1.12 - 2024-04-30
move validator functions from gDRcomponents to gDRutils
gDRutils 1.1.11 - 2024-04-15
add get_testdata_combo and get_testdata_codilution
gDRutils 1.1.10 - 2024-03-07
gDRutils 1.1.9 - 2024-03-07
gDRutils 1.1.8 - 2024-02-28
add fit_source to header list
gDRutils 1.1.7 - 2024-02-26
improve pkgdown site
improved references
valid NEWS.md
gDRutils 1.1.6 - 2024-02-22
restore tooltips in table
gDRutils 1.1.5 - 2024-02-14
make documentation compatible with pkdgdown
gDRutils 1.1.4 - 2024-01-30
rename matrix into combination
gDRutils 1.1.3 - 2024-01-22
add new description fields
gDRutils 1.1.2 - 2023-12-01
fix bug with refining rowData
extend the list of headers
gDRutils 1.1.1 - 2023-11-22
sync master with devel branch
update schema to support NA in reference division time
add minor fix in code styling
add new function gemoetric_mean
transform values into numeric in predict_efficacy_from_conc function
add “Treatment” as template identifier
gDRutils 1.1.0 - 2023-10-24
gDRutils 1.0.0 - 2023-10-24
prepare prerelease for Bioc 3.18
gDRutils 0.99.34 - 2023-10-18
adjust NEWS to Bioc format
gDRutils 0.99.33 - 2023-10-09
add support for flattening averaged assays
gDRutils 0.99.32 - 2023-09-22
fix bug in the case of conc=0 for evaluating efficacy
gDRutils 0.99.31 - 2023-09-19
add wide_structure param to convert_mae_assay_to_dt
gDRutils 0.99.30 - 2023-09-08
update experimentalist description in schema
gDRutils 0.99.29 - 2023-09-05
add Replicate as a new identifier
gDRutils 0.99.28 - 2023-09-05
improve the logic of standardize_MAE to keep SE-specific metadata and be able to revert standardization
gDRutils 0.99.27 - 2023-08-01
keep unchanged names in DataFrame
gDRutils 0.99.26 - 2023-08-01
gDRutils 0.99.25 - 2023-06-27
add assert for missing rownames
gDRutils 0.99.24 - 2023-06-22
gDRutils 0.99.23 - 2023-06-20
gDRutils 0.99.22 - 2023-06-12
gDRutils 0.99.21 - 2023-06-12
gDRutils 0.99.20 - 2023-06-07
switch from aggregate to data.table
gDRutils 0.99.19 - 2023-06-06
replace reshape2 functions by functions from data.table
gDRutils 0.99.18 - 2023-05-22
format the vignette with BiocStyle
gDRutils 0.99.17 - 2023-05-22
fix related with data.table
remove .get_treated_conditions and .get_untreated_conditions
gDRutils 0.99.16 - 2023-05-18
add support for merging combination-data assays
gDRutils 0.99.15 - 2023-05-12
update after unifying normalization types
gDRutils 0.99.14 - 2023-05-12
gDRutils 0.99.13 - 2023-05-09
removed cotreatment entry from EXPERIMENT_GROUPS
gDRutils 0.99.12 - 2023-05-09
fix bug in convert_mae_assay_to_dt
gDRutils 0.99.11 - 2023-05-08
refactor code with single ampersand in if statements
gDRutils 0.99.10 - 2023-04-28
change order of untreated tags
gDRutils 0.99.9 - 2023-04-24
changed data.frame to data.table
gDRutils 0.99.8 - 2023-04-20
gDRutils 0.99.7 - 2023-04-20
gDRutils 0.99.6 - 2023-04-18
extend the logic of apply_bumpy_function
gDRutils 0.99.5 - 2023-04-17
add R 4.2 as a dependency
gDRutils 0.99.4 - 2023-04-14
gDRutils 0.99.3 - 2023-04-13
gDRutils 0.99.2 - 2023-04-12
gDRutils 0.99.1 - 2023-04-07
gDRutils 0.99.0 - 2023-03-28
downgrade version to make it Bioconductor compatible
gDRutils 0.1.3.22 - 2023-03-13
gDRutils 0.1.3.21 - 2023-03-09
better handling of corner cases for the single-agent fitting
gDRutils 0.1.3.20 - 2023-03-08
add support for splitting normalization data types
gDRutils 0.1.3.19 - 2023-03-08
restore necessary functions
gDRutils 0.1.3.18 - 2023-03-01
add examples of identifiers
gDRutils 0.1.3.17 - 2023-03-01
gDRutils 0.1.3.16 - 2023-02-22
gDRutils 0.1.3.15 - 2023-02-10
add tests for convert_se_ref_assay_to_dt
gDRutils 0.1.3.14 - 2023-01-10
add helpers for colData/rowData refinement
gDRutils 0.1.3.13 - 2022-12-22
fix warnings in unit tests
gDRutils 0.1.3.12 - 2022-12-20
R CMD check returns 0 errors ✓ | 0 warnings ✓ | 0 notes ✓
gDRutils 0.1.3.11 - 2022-12-15
default apply_bumpy_function parallelize to TRUE
gDRutils 0.1.3.10 - 2022-12-08
add apply_bumpy_function support
gDRutils 0.1.3.9 - 2022-12-07
add co-dilution to single-agent group
gDRutils 0.1.3.8 - 2022-11-30
gDRutils 0.1.3.7 - 2022-10-18
add update_env_idfs_from_mae function
gDRutils 0.1.3.6 - 2022-10-04
add helper for dealing with idfs’ synonyms
gDRutils 0.1.3.5 - 2022-09-21
promote or demote fields in a BumpyMatrix object and perform summarization on assays.
gDRutils 0.1.3.4 - 2022-08-11
major improvements in JSON validation/conversion logic
provide info about JSON schemes via env variables
convert and validate MAE summary next to the SE experiments
gDRutils 0.1.3.3 - 2022-07-25
move json validation/conversion logic from gDRelastic
gDRutils 0.1.3.2 - 2022-07-11
standardize MAE using default gDR identifiers
gDRutils 0.1.3.1 - 2022-06-29
remove adding integer identifiers at the end of colnames/rownames
gDRutils 0.1.3.0 - 2022-06-02
gDRutils 0.1.0.48 - 2022-05-27
correct recognition of empty SE
gDRutils 0.1.0.47 - 2022-05-25
remove redundant validation of rownames in SE
gDRutils 0.1.0.46 - 2022-05-03
update prettify function
fix hardcoded identifiers in validated_SE
gDRutils 0.1.0.45 - 2022-04-29
avoid using grep for getting cotreatment identifiers
gDRutils 0.1.0.44 - 2022-04-26
switched from unnamed to named vector of experiment groups for single-agent
fix the logic in validating single-agent experiments
gDRutils 0.1.0.43 - 2022-04-13
set r2 value to NA for invalid and 0 for constant fits
gDRutils 0.1.0.42 - 2022-04-08
add identifier descriptions
gDRutils 0.1.0.41 - 2022-04-08
fix wrong order of elements in rownames in SE
gDRutils 0.1.0.40 - 2022-04-07
gDRutils 0.1.0.39 - 2022-03-31
extend possible Barcode identifiers
gDRutils 0.1.0.38 - 2022-03-30
fix hardcoded identifiers in validate SE
gDRutils 0.1.0.37 - 2022-03-28
add a space between two-word cotreatment identifiers
gDRutils 0.1.0.36 - 2022-03-24
remove all R CMD check warnings
gDRutils 0.1.0.35 - 2022-03-22
change prettify functions to not substitute metadata
gDRutils 0.1.0.34 - 2022-03-21
add helper function for MAE/experiments
gDRutils 0.1.0.33 - 2022-03-19
move constant fit warning
gDRutils 0.1.0.32 - 2022-03-18
add .calculate_complement
gDRutils 0.1.0.31 - 2022-03-16
gDRutils 0.1.0.30 - 2022-03-14
add support for identifier validation
gDRutils 0.1.0.29 - 2022-03-03
add getter and setter for experiment_raw_data
gDRutils 0.1.0.28 - 2022-02-16
refactor identifier drugname to drug_name
gDRutils 0.1.0.27 - 2022-02-10
gDRutils 0.1.0.26 - 2022-02-01
gDRutils 0.1.0.25 - 2022-01-31
support SE- init for different BioC versions
gDRutils 0.1.0.24 - 2022-01-25
gDRutils 0.1.0.23 - 2022-01-25
switch unit tests from SE to MAE from gDRtestData
gDRutils 0.1.0.22 - 2022-01-07
update assert in validate_MAE
gDRutils 0.1.0.21 - 2022-01-07
update SE-related functions of gDRutils to support MAE
gDRutils 0.1.0.20 - 2021-12-21
move combo-related functions from gDRviz
add unit tests for combo-related functions
gDRutils 0.1.0.19 - 2021-11-04
do not create a nested list of identifiers during merging SE
gDRutils 0.1.0.18 - 2021-11-01
fix issued with new SummarizedExperiment
gDRutils 0.1.0.17 - 2021-10-22
refactor: generalize prediction help functions for fits
gDRutils 0.1.0.16 - 2021-09-27
update validate_SE as per combos
gDRutils 0.1.0.15 - 2021-09-22
feat: use ‘GRvalue’ and ‘RelativeViability’ as normalization_types in ‘fit_curves’
gDRutils 0.1.0.14 - 2021-09-15
fix bug with getting_SE_identifiers for untreated_tag
gDRutils 0.1.0.13 - 2021-09-13
fix obsolete arguments in reset_env_identifiers
gDRutils 0.1.0.12 - 2021-09-07
fix bug with getting identifiers for untreated_tag
gDRutils 0.1.0.11 - 2021-08-26
move NA logic for elements of BumpyMatrix with no data to fit_curve
gDRutils 0.1.0.10 - 2021-08-25
remove additional ordering line in df_to_bm_assay.R
gDRutils 0.1.0.9 - 2021-08-19
update list of available identifiers - 2nd and 3rd drug, data_source
update the logic for get_identifier and .get_id
add prettified_identifier-
gDRutils 0.1.0.8 - 2021-08-13
fix bug with wrong order of rows and cols in df_to_bm_assay
gDRutils 0.1.0.7 - 2021-07-06
remove hard version equality for pkg deps
gDRutils 0.1.0.6 - 2021-06-29
add barcode as identifiers and store identifiers within split_SE_components
gDRutils 0.1.0.5 - 2021-06-25
update the logic for CI/CD - repos fetching is now handled with technical user
gDRutils 0.1.0.4 - 2021-06-18
add concentration and template as additional identifiers
gDRutils 0.1.0.3 - 2021-06-21
refactor logisticFit with error handling
gDRutils 0.1.0.2 - 2021-06-18
remove deprecated functions
switch from getMetadata to split_SE_components
refactor df_to_bm_assay
gDRutils 0.1.0.1 - 2021-06-02
upgrade validate_SE by checking if rowData and colData do not have empty strings
isolate flatten function
gDRutils 0.1.0.0 - 2021-06-02
gDRutils 0.0.0.49 - 2021-06-02
fix bug with merging flatten assays
gDRutils 0.0.0.48 - 2021-05-24
refactor validate_SE function
gDRutils 0.0.0.47 - 2021-05-18
gDRutils 0.0.0.46 - 2021-05-18
fix typo in SE validator function
gDRutils 0.0.0.45 - 2021-05-18
add SE validator function
gDRutils 0.0.0.44 - 2021-05-13
refactor prettify_flat_metrics function
gDRutils 0.0.0.43 - 2021-04-30
remove Metrics_rownames during flattening data.frame/data.table
gDRutils 0.0.0.42 - 2021-04-29
add prettify_flat_metrics function
gDRutils 0.0.0.41 - 2021-04-29
fix flattening data.tables
gDRutils 0.0.0.40 - 2021-04-29
fix data.table merge in convert_se_assay_ref_to_dt
gDRutils 0.0.0.39 - 2021-04-27
add support for flattening data.tables
gDRutils 0.0.0.38 - 2021-04-21
switch from processing_metadata to .internal
gDRutils 0.0.0.37 - 2021-04-20
add support for getting and setting processing info metadata
gDRutils 0.0.0.36 - 2021-04-19
sort BumpyMatrix created from dt
gDRutils 0.0.0.35 - 2021-04-14
revert metric arguments in ‘convert_se_assay_to_dt’
gDRutils 0.0.0.34 - 2021-04-09
add support for getting and setting fit parameter metadata
gDRutils 0.0.0.33 - 2021-04-07
standardize metric header names
gDRutils 0.0.0.32 - 2021-04-07
add more options for returned data - with ‘Metrics’ assay in the case of convert_se_assay_to_dt
add ‘convert_se_ref_assay_to_dt’ function
gDRutils 0.0.0.31 - 2021-03-30
add support for getting and setting metadata on the SummarizedExperiment object
gDRutils 0.0.0.30 - 2021-03-30
add support for getting and setting metadata on the SummarizedExperiment object
add numeric type assertions and tests for logistic_4parameters
gDRutils 0.0.0.29 - 2021-03-23
remove positional naming dependence on assay_to_dt for - merge_metrics = TRUE argument
gDRutils 0.0.0.28 - 2021-03-16
refactor to assay_to_dt
deprecated support for assay_to_dt- include_controls = TRUE argument - not backwards compatible
gDRutils 0.0.0.27 - 2021-03-09
update .estimate_xc50 and add tests
gDRutils 0.0.0.26 - 2021-03-04
fix bug with wrong class for S3 methods in convert_assay_data_to_dt
update the documentation
gDRutils 0.0.0.25 - 2021-03-02
fix bug with missing class in assert for matrix
gDRutils 0.0.0.24 - 2021-02-10
modify fit_curves to take in flexible curve_type- s
clean-up assay_to_dt
gDRutils 0.0.0.23 - 2021-02-04
gDRutils 0.0.0.22 - 2021-02-03
move assay_to_dt from gDR to gDRutils
refactor assay_to_dt to support two assay types
list of DFrame- s
BumpyMatrix objects
move .get_treated_conditions and .get_untreated_conditions from gDR to gDRutils
gDRutils 0.0.0.21 - 2021-01-26
allow for DFrame as input
gDRutils 0.0.0.20 - 2021-01-26
‘s/BumpyMatrix::splitToBumpyMatrix/BumpyMatrix::splitAsBumpyMatrix/’
gDRutils 0.0.0.19 - 2021-01-20
refactor RVGRfits and rename to fit_curves
make logisticFit function independent of curve_type
gDRutils 0.0.0.18 - 2021-01-19
move df_to_assay.R from gDRcore to gDRutils
move df_to_bm_assay.R from gDRcore to gDRutils
update identifiers_list.R
gDRutils 0.0.0.15 - 2020-12-14
refactor get_identifiers and get_headers to be settable and cached
gDRutils 0.0.0.14 - 2020-12-14
totally, finally, and unscrupulously remove dplyr package from gDRutils
replace IC by RV
gDRutils 0.0.0.13 - 2020-10-12
gDRutils 0.0.0.12 - 2020-10-09
gDRutils 0.0.0.11 - 2020-10-09
gDRutils 0.0.0.10 - 2020-10-05
gDRutils 0.0.0.9 - 2020-09-14
add small fixes for assays with empty DataFrame
gDRutils 0.0.0.8 - 2020-09-02
update logic as per new db model
gDRutils 0.0.0.7 - 2020-08-07
update variable names as per new db model
gDRutils 0.0.0.6 - 2020-07-02
import pipes from magrittr
gDRutils 0.0.0.4 - 2020-06-10
including the masked field to be able to remove the masked data from averages