Changes in version 2024-12-10 (2024-12-10) - make split_SE_components working correctly for sa assay data, modified with avearge_biological_duplicates Changes in version 2024-12-09 (2024-12-09) - minor improvement in the logic of average_biological_replicates (new blacklisted column) Changes in version 2024-12-02 (2024-12-02) - refactor set_unique_* functions Changes in version 2024-11-05 (2024-11-05) - add get_env_var helper - synchronize Bioconductor and GitHub versioning Changes in version 2024-10-24 (2024-10-24) - make average_biological_replicates_dt more restrictive - fewer columns to check for duplicates Changes in version 2024-10-11 (2024-10-11) - make duplicates' helpers supporting combo assays as well Changes in version 2024-10-07 (2024-10-07) - refactor the logic for dealing with duplicates in assay data Changes in version 2024-10-03 (2024-10-03) - fixed issue in average_biological_replicated (fit_type) Changes in version 2024-09-16 (2024-09-16) - add functions set_unique_cl_names_dt and set_unique_drug_names_dt Changes in version 2024-09-04 (2024-09-04) - remove hack with checkDimnames Changes in version 2024-08-30 (2024-08-30) - remove GDS fit_source from gDRviz Changes in version 2024-08-28 (2024-08-28) - extend the logic of get_additional_variables to support other sources of fitting metrics Changes in version 2024-08-14 (2024-08-14) - extend the logic of average_biological_replicates_dt to calculate standard deviation Changes in version 2024-08-06 (2024-08-06) - add functions for setting unique identifiers in the colData and rowData of SE Changes in version 2024-07-30 (2024-07-30) - refactor average_biological_replicates_dt and get_additional_variables to support unprettified identifiers Changes in version 2024-07-17 (2024-07-17) - update define_matrix_grid_positions Changes in version 2024-07-12 (2024-07-12) - move get_combo_col_settings and get_iso_colors to gDRplots package Changes in version 2024-07-08 (2024-07-08) - add residual sum of square and p-value to Metrics assay Changes in version 2024-07-03 (2024-07-03) - add vignette section about prettifying logic Changes in version 2024-06-24 (2024-06-24) - fixed issue in vignette Changes in version 2024-05-27 (2024-05-27) - synchronize Bioconductor and GitHub versioning Changes in version 2024-05-22 (2024-05-22) - fix check notes - move convert_se_assay_to_custom_dt, capVals and get_settings_from_json from gDRcomponents package Changes in version 2024-05-17 (2024-05-17) - simplify logic of supported experiments Changes in version 2024-05-16 (2024-05-16) - move define_matrix_grid_positions and round_concentration functions from gDRcore package Changes in version 2024-05-08 (2024-05-08) - fix typo Changes in version 2024-04-30 (2024-04-30) - move validator functions from gDRcomponents to gDRutils Changes in version 2024-04-15 (2024-04-15) - add get_testdata_combo and get_testdata_codilution Changes in version 2024-03-07 (2024-03-07) - clean up the package - simplify keywords Changes in version 2024-02-28 (2024-02-28) - add fit_source to header list Changes in version 2024-02-26 (2024-02-26) - improve pkgdown site - improved references - valid NEWS.md Changes in version 2024-02-22 (2024-02-22) - restore tooltips in table Changes in version 2024-02-14 (2024-02-14) - make documentation compatible with pkdgdown Changes in version 2024-01-30 (2024-01-30) - rename matrix into combination Changes in version 2024-01-22 (2024-01-22) - add new description fields Changes in version 2023-12-01 (2023-12-01) - fix bug with refining rowData - extend the list of headers Changes in version 2023-11-22 (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 Changes in version 2023-10-24 (2023-10-24) - release Bioc 3.18 - prerelease Bioc 3.18 Changes in version 2023-10-18 (2023-10-18) - adjust NEWS to Bioc format Changes in version 2023-10-09 (2023-10-09) - add support for flattening averaged assays Changes in version 2023-09-22 (2023-09-22) - fix bug in the case of conc=0 for evaluating efficacy Changes in version 2023-09-19 (2023-09-19) - add wide_structure param to convert_mae_assay_to_dt Changes in version 2023-09-08 (2023-09-08) - updated experimentalist description in schema Changes in version 2023-09-05 (2023-09-05) - add Replicate as a new identifier - improve the logic of standardize_MAE to keep SE-specific metadata and be able to revert standardization Changes in version 2023-08-01 (2023-08-01) - keep unchanged names in DataFrame - tidy code Changes in version 2023-06-27 (2023-06-27) - add assert for missing rownames Changes in version 2023-06-22 (2023-06-22) - replaced RDS with qs Changes in version 2023-06-20 (2023-06-20) - fix check in R 4.3 Changes in version 2023-06-12 (2023-06-12) - switch from merge to [[ - replace order with data.table::setorder - add support for custom identifiers in merge_SE Changes in version 2023-06-07 (2023-06-07) - switch from aggregate to data.table Changes in version 2023-06-06 (2023-06-06) - replaced reshape2 functions by functions from data.table Changes in version 2023-05-22 (2023-05-22) - format the vignette with BiocStyle - fix related with data.table - remove .get_treated_conditions and .get_untreated_conditions Changes in version 2023-05-18 (2023-05-18) - add support for merging combination-data assays Changes in version 2023-05-12 (2023-05-12) - update after unifying normalization types - fix lintr Changes in version 2023-05-09 (2023-05-09) - removed cotreatment entry from EXPERIMENT_GROUPS - fix bug in convert_mae_assay_to_dt Changes in version 2023-05-08 (2023-05-08) - refactor code with single ampersand in if statements Changes in version 2023-04-28 (2023-04-28) - change order of untreated tags Changes in version 2023-04-24 (2023-04-24) - changed data.frame to data.table Changes in version 2023-04-20 (2023-04-20) - switch to OSI license - clean-up vignette Changes in version 2023-04-18 (2023-04-18) - extend the logic of apply_bumpy_function Changes in version 2023-04-17 (2023-04-17) - add R 4.2 as a dependency Changes in version 2023-04-14 (2023-04-14) - fix examples Changes in version 2023-04-13 (2023-04-13) - make linter happy Changes in version 2023-04-12 (2023-04-12) - add license Changes in version 2023-04-07 (2023-04-07) - update maintainer Changes in version 2023-03-28 (2023-03-28) - downgrade version to make it Bioconductor compatible Changes in version 2023-03-13 (2023-03-13) - tidy code Changes in version 2023-03-09 (2023-03-09) - better handling of corner cases for the single-agent fitting Changes in version 2023-03-08 (2023-03-08) - add support for splitting normalization data types - restore necessary functions Changes in version 2023-03-01 (2023-03-01) - add examples of identifiers - remove obsolete code Changes in version 2023-02-22 (2023-02-22) - tidy code Changes in version 2023-02-10 (2023-02-10) - add tests for convert_se_ref_assay_to_dt Changes in version 2023-01-10 (2023-01-10) - add helpers for colData/rowData refinement Changes in version 2022-12-22 (2022-12-22) - fix warnings in unit tests Changes in version 2022-12-20 (2022-12-20) - R CMD check returns 0 errors ✓ | 0 warnings ✓ | 0 notes ✓ Changes in version 2022-12-15 (2022-12-15) - default apply_bumpy_function parallelize to TRUE Changes in version 2022-12-08 (2022-12-08) - add apply_bumpy_function support Changes in version 2022-12-07 (2022-12-07) - add co-dilution to single-agent group Changes in version 2022-11-30 (2022-11-30) - bugfix in validate_SE Changes in version 2022-10-18 (2022-10-18) - add update_env_idfs_from_mae function Changes in version 2022-10-04 (2022-10-04) - add helper for dealing with idfs' synonyms Changes in version 2022-09-21 (2022-09-21) - promote or demote fields in a BumpyMatrix object and perform summarization on assays. Changes in version 2022-08-11 (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 Changes in version 2022-07-25 (2022-07-25) - move json validation/conversion logic from gDRelastic Changes in version 2022-07-11 (2022-07-11) - standardize MAE using default gDR identifiers Changes in version 2022-06-29 (2022-06-29) - remove adding integer identifiers at the end of colnames/rownames Changes in version 2022-06-02 (2022-06-02) - release 1.3.0 Changes in version 2022-05-27 (2022-05-27) - correct recognition of empty SE Changes in version 2022-05-25 (2022-05-25) - remove redundant validation of rownames in SE Changes in version 2022-05-03 (2022-05-03) - update prettify function - fix hardcoded identifiers in validated_SE Changes in version 2022-04-29 (2022-04-29) - avoid using grep for getting cotreatment identifiers Changes in version 2022-04-26 (2022-04-26) - switched from unnamed to named vector of experiment groups for single-agent - fix the logic in validating single-agent experiments Changes in version 2022-04-13 (2022-04-13) - set r2 value to NA for invalid and 0 for constant fits Changes in version 2022-04-08 (2022-04-08) - added identifier descriptions - fix wrong order of elements in rownames in SE Changes in version 2022-04-07 (2022-04-07) - add cap_ic50 function Changes in version 2022-03-31 (2022-03-31) - extend possible Barcode identifiers Changes in version 2022-03-30 (2022-03-30) - fix hardcoded identifiers in validate SE Changes in version 2022-03-28 (2022-03-28) - add a space between two-word cotreatment identifiers Changes in version 2022-03-24 (2022-03-24) - remove all R CMD check warnings Changes in version 2022-03-22 (2022-03-22) - change prettify functions to not substitute metadata Changes in version 2022-03-21 (2022-03-21) - add helper function for MAE/experiments Changes in version 2022-03-19 (2022-03-19) - move constant fit warning Changes in version 2022-03-18 (2022-03-18) - add .calculate_complement Changes in version 2022-03-16 (2022-03-16) - move duplication warning Changes in version 2022-03-14 (2022-03-14) - add support for identifier validation Changes in version 2022-03-03 (2022-03-03) - add getter and setter for experiment_raw_data Changes in version 2022-02-16 (2022-02-16) - refactor identifier drugname to drug_name Changes in version 2022-02-10 (2022-02-10) - add MAEpply function Changes in version 2022-02-01 (2022-02-01) - update documentation Changes in version 2022-01-31 (2022-01-31) - support SE- init for different BioC versions Changes in version 2022-01-25 (2022-01-25) - standardize/improve CI - switch unit tests from SE to MAE from gDRtestData Changes in version 2022-01-07 (2022-01-07) - update assert in validate_MAE - update SE-related functions of gDRutils to support MAE Changes in version 2021-12-21 (2021-12-21) - move combo-related functions from gDRviz - add unit tests for combo-related functions Changes in version 2021-11-04 (2021-11-04) - do not create a nested list of identifiers during merging SE Changes in version 2021-11-01 (2021-11-01) - fix issued with new SummarizedExperiment Changes in version 2021-10-22 (2021-10-22) - refactor: generalize prediction help functions for fits Changes in version 2021-09-27 (2021-09-27) - update validate_SE as per combos Changes in version 2021-09-22 (2021-09-22) - feat: use 'GRvalue' and 'RelativeViability' as normalization_types in 'fit_curves' Changes in version 2021-09-15 (2021-09-15) - fix bug with getting_SE_identifiers for untreated_tag Changes in version 2021-09-13 (2021-09-13) - fix obsolete arguments in reset_env_identifiers Changes in version 2021-09-07 (2021-09-07) - fix bug with getting identifiers for untreated_tag Changes in version 2021-08-26 (2021-08-26) - move NA logic for elements of BumpyMatrix with no data to fit_curve Changes in version 2021-08-25 (2021-08-25) - remove additional ordering line in df_to_bm_assay.R Changes in version 2021-08-19 (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- Changes in version 2021-08-13 (2021-08-13) - fix bug with wrong order of rows and cols in df_to_bm_assay Changes in version 2021-07-06 (2021-07-06) - remove hard version equality for pkg deps Changes in version 2021-06-29 (2021-06-29) - add barcode as identifiers and store identifiers within split_SE_components Changes in version 2021-06-25 (2021-06-25) - update the logic for CI/CD - repos fetching is now handled with technical user Changes in version 2021-06-21 (2021-06-21) - refactor logisticFit with error handling Changes in version 2021-06-18 (2021-06-18) - add concentration and template as additional identifiers - remove deprecated functions - switch from getMetadata to split_SE_components - refactor df_to_bm_assay Changes in version 2021-06-02 (2021-06-02) - upgrade validate_SE by checking if rowData and colData do not have empty strings - isolate flatten function - release 1.0.0 - fix bug with merging flatten assays Changes in version 2021-05-24 (2021-05-24) - refactor validate_SE function Changes in version 2021-05-18 (2021-05-18) - add merge_SE function - fix typo in SE validator function - add SE validator function Changes in version 2021-05-13 (2021-05-13) - refactor prettify_flat_metrics function Changes in version 2021-04-30 (2021-04-30) - remove Metrics_rownames during flattening data.frame/data.table Changes in version 2021-04-29 (2021-04-29) - add prettify_flat_metrics function - bugfix flattening data.tables - bugfix data.table merge in convert_se_assay_ref_to_dt Changes in version 2021-04-27 (2021-04-27) - add support for flattening data.tables Changes in version 2021-04-21 (2021-04-21) - switch from processing_metadata to .internal Changes in version 2021-04-20 (2021-04-20) - add support for getting and setting processing info metadata Changes in version 2021-04-19 (2021-04-19) - sort BumpyMatrix created from dt Changes in version 2021-04-14 (2021-04-14) - revert metric arguments in 'convert_se_assay_to_dt' Changes in version 2021-04-09 (2021-04-09) - add support for getting and setting fit parameter metadata Changes in version 2021-04-07 (2021-04-07) - standardize metric header names - 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 Changes in version 2021-03-30 (2021-03-30) - add support for getting and setting metadata on the SummarizedExperiment object - add support for getting and setting metadata on the SummarizedExperiment object - add numeric type assertions and tests for logistic_4parameters Changes in version 2021-03-23 (2021-03-23) - remove positional naming dependence on assay_to_dt for - merge_metrics = TRUE argument Changes in version 2021-03-16 (2021-03-16) - minor refactor to assay_to_dt - deprecated support for assay_to_dt- include_controls = TRUE argument - not backwards compatible Changes in version 2021-03-09 (2021-03-09) - update .estimate_xc50 and add tests Changes in version 2021-03-04 (2021-03-04) - fix bug with wrong class for S3 methods in convert_assay_data_to_dt - update the documentation Changes in version 2021-03-02 (2021-03-02) - fix bug with missing class in assert for matrix Changes in version 2021-02-10 (2021-02-10) - modify fit_curves to take in flexible curve_type- s - clean-up assay_to_dt Changes in version 2021-02-04 (2021-02-04) - added linter Changes in version 2021-02-03 (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 Changes in version 2021-01-26 (2021-01-26) - allow for DFrame as input - 's/BumpyMatrix::splitToBumpyMatrix/BumpyMatrix::splitAsBumpyMatrix/' Changes in version 2021-01-20 (2021-01-20) - refactor RVGRfits and rename to fit_curves - make logisticFit function independent of curve_type Changes in version 2021-01-19 (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 Changes in version 2020-12-14 (2020-12-14) - refactor get_identifiers and get_headers to be settable and cached - totally, finally, and unscrupulously remove dplyr package from gDRutils - replace IC by RV Changes in version 2020-10-12 (2020-10-12) - add CI Changes in version 2020-10-09 (2020-10-09) - fix assay_to_df - update namespaces Changes in version 2020-10-05 (2020-10-05) - minor refactor Changes in version 2020-09-14 (2020-09-14) - add small fixes for assays with empty DataFrame Changes in version 2020-09-02 (2020-09-02) - update logic as per new db model Changes in version 2020-08-07 (2020-08-07) - update variable names as per new db model Changes in version 2020-07-02 (2020-07-02) - import pipes from magrittr Changes in version 2020-06-10 (2020-06-10) - including the masked field to be able to remove the masked data from averages