Changes in version 0.99.34 (2023-10-18) - adjust NEWS to Bioc format Changes in version 0.99.33 (2023-10-09) - add support for flattening averaged assays Changes in version 0.99.32 (2023-09-22) - fix bug in the case of conc=0 for evaluating efficacy Changes in version 0.99.31 (2023-09-19) - add wide_structure param to convert_mae_assay_to_dt Changes in version 0.99.30 (2023-09-08) - updated experimentalist description in schema Changes in version 0.99.29 (2023-09-05) - add Replicate as a new identifier Changes in version 0.99.28 (2023-09-05) - improve the logic of standardize_MAE to keep SE-specific metadata and be able to revert standardization Changes in version 0.99.27 (2023-08-01) - keep unchanged names in DataFrame Changes in version 0.99.26 (2023-08-01) - tidy code Changes in version 0.99.25 (2023-06-27) - add assert for missing rownames Changes in version 0.99.24 (2023-06-22) - replaced RDS with qs Changes in version 0.99.23 (2023-06-20) - fix check in R 4.3 Changes in version 0.99.22 (2023-06-12) - switch from merge to [[ Changes in version 0.99.21 (2023-06-12) - replace order with data.table::setorder - add support for custom identifiers in merge_SE Changes in version 0.99.20 (2023-06-07) - switch from aggregate to data.table Changes in version 0.99.19 (2023-06-06) - replaced reshape2 functions by functions from data.table Changes in version 0.99.18 (2023-05-22) - format the vignette with BiocStyle Changes in version 0.99.17 (2023-05-22) - fix related with data.table - remove .get_treated_conditions and .get_untreated_conditions Changes in version 0.99.16 (2023-05-18) - add support for merging combination-data assays Changes in version 0.99.15 (2023-05-12) - update after unifying normalization types Changes in version 0.99.14 (2023-05-12) - fix lintr Changes in version 0.99.13 (2023-05-09) - removed cotreatment entry from EXPERIMENT_GROUPS Changes in version 0.99.12 (2023-05-09) - fix bug in convert_mae_assay_to_dt Changes in version 0.99.11 (2023-05-08) - refactor code with single ampersand in if statements Changes in version 0.99.10 (2023-04-28) - change order of untreated tags Changes in version 0.99.9 (2023-04-24) - changed data.frame to data.table Changes in version 0.99.8 (2023-04-20) - switch to OSI license Changes in version 0.99.7 (2023-04-20) - clean-up vignette Changes in version 0.99.6 (2023-04-18) - extend the logic of apply_bumpy_function Changes in version 0.99.5 (2023-04-17) - add R 4.2 as a dependency Changes in version 0.99.4 (2023-04-14) - fix examples Changes in version 0.99.3 (2023-04-13) - make linter happy Changes in version 0.99.2 (2023-04-12) - add licence Changes in version 0.99.1 (2023-04-07) - update maintainer Changes in version 0.99.0 (2023-03-28) - downgrade version to make it Bioconductor compatible Changes in version 0.1.3.22 (2023-03-13) - tidy code Changes in version 0.1.3.21 (2023-03-09) - better handling of corner cases for the single-agent fitting Changes in version 0.1.3.20 (2023-03-08) - add support for splitting normalization data types Changes in version 0.1.3.19 (2023-03-08) - restore necessary functions Changes in version 0.1.3.18 (2023-03-01) - add examples of identifiers Changes in version 0.1.3.17 (2023-03-01) - remove obsolete code Changes in version 0.1.3.16 (2023-02-22) - tidy code Changes in version 0.1.3.15 (2023-02-10) - add tests for convert_se_ref_assay_to_dt Changes in version 0.1.3.14 (2023-01-10) - add helpers for colData/rowData refinement Changes in version 0.1.3.13 (2022-12-22) - fix warnings in unit tests Changes in version 0.1.3.12 (2022-12-20) - R CMD check returns 0 errors ✓ | 0 warnings ✓ | 0 notes ✓ Changes in version 0.1.3.11 (2022-12-15) - default apply_bumpy_function parallelize to TRUE Changes in version 0.1.3.10 (2022-12-08) - add apply_bumpy_function support Changes in version 0.1.3.9 (2022-12-07) - add co-dilution to single-agent group Changes in version 0.1.3.8 (2022-11-30) - bugfix in validate_SE Changes in version 0.1.3.7 (2022-10-18) - add update_env_idfs_from_mae function Changes in version 0.1.3.6 (2022-10-04) - add helper for dealing with idfs' synonyms Changes in version 0.1.3.5 (2022-09-21) - promote or demote fields in a BumpyMatrix object and perform summarization on assays. Changes in version 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 Changes in version 0.1.3.3 (2022-07-25) - move json validation/convertion logic from gDRelastic Changes in version 0.1.3.2 (2022-07-11) - standardize MAE using default gDR identifiers Changes in version 0.1.3.1 (2022-06-29) - remove adding integer identifiers at the end of colnames/rownames Changes in version 0.1.3.0 (2022-06-02) - release 1.3.0 Changes in version 0.1.0.48 (2022-05-27) - correct recognition of empty SE Changes in version 0.1.0.47 (2022-05-25) - remove redundant validation of rownames in SE Changes in version 0.1.0.46 (2022-05-03) - update prettify function - fix hardcoded identifiers in validated_SE Changes in version 0.1.0.45 (2022-04-29) - avoid using grep for getting cotreatment identifiers Changes in version 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 Changes in version 0.1.0.43 (2022-04-13) - set r2 value to NA for invalid and 0 for constant fits Changes in version 0.1.0.42 (2022-04-08) - added identifier descriptions Changes in version 0.1.0.41 (2022-04-08) - fix wrong order of elements in rownames in SE Changes in version 0.1.0.40 (2022-04-07) - add cap_ic50 function Changes in version 0.1.0.39 (2022-03-31) - extend possible Barcode identifiers Changes in version 0.1.0.38 (2022-03-30) - fix hardcoded identifiers in validate SE Changes in version 0.1.0.37 (2022-03-28) - added a space between two-word cotreatment identifiers Changes in version 0.1.0.36 (2022-03-24) - remove all R CMD check warnings Changes in version 0.1.0.35 (2022-03-22) - change prettify functions to not substitute metadata Changes in version 0.1.0.34 (2022-03-21) - add helper function for MAE/experiments Changes in version 0.1.0.33 (2022-03-19) - move constant fit warning Changes in version 0.1.0.32 (2022-03-18) - add .calculate_complement Changes in version 0.1.0.31 (2022-03-16) - move duplication warning Changes in version 0.1.0.30 (2022-03-14) - add support for identifier validation Changes in version 0.1.0.29 (2022-03-03) - add getter and setter for experiment_raw_data Changes in version 0.1.0.28 (2022-02-16) - refactor identifier drugname to drug_name Changes in version 0.1.0.27 (2022-02-10) - add MAEpply function Changes in version 0.1.0.26 (2022-02-01) - update documentation Changes in version 0.1.0.25 (2022-01-31) - support SE() init for different BioC versions Changes in version 0.1.0.24 (2022-01-25) - standardize/improve CI Changes in version 0.1.0.23 (2022-01-25) - switch unit tests from SE to MAE from gDRtestData Changes in version 0.1.0.22 (2022-01-07) - update assert in validate_MAE Changes in version 0.1.0.21 (2022-01-07) - update SE-related functions of gDRutils to support MAE Changes in version 0.1.0.20 (2021-12-21) - move combo-related functions from gDRviz - add unit tests for combo-related functions Changes in version 0.1.0.19 (2021-11-04) - do not create a nested list of identifiers during mergin SE Changes in version 0.1.0.18 (2021-11-01) - fix issued with new SummarizedExperiment Changes in version 0.1.0.17 (2021-10-22) - refactor: generalize prediction help functions for fits Changes in version 0.1.0.16 (2021-09-27) - update validate_SE as per combos Changes in version 0.1.0.15 (2021-09-22) - feat: use 'GRvalue' and 'RelativeViability' as normalization_types in 'fit_curves' Changes in version 0.1.0.14 (2021-09-15) - fix bug with getting_SE_identifiers for untreated_tag Changes in version 0.1.0.13 (2021-09-13) - fix obsolete arguments in reset_env_identifiers Changes in version 0.1.0.12 (2021-09-07) - fix bug with getting identifiers for untreated_tag Changes in version 0.1.0.11 (2021-08-26) - move NA logic for elements of BumpyMatrix with no data to fit_curve Changes in version 0.1.0.10 (2021-08-25) - remove additional ordering line in df_to_bm_assay.R Changes in version 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() Changes in version 0.1.0.8 (2021-08-13) - fix bug with wrong order of rows and cols in df_to_bm_assay Changes in version 0.1.0.7 (2021-07-06) - remove hard version equality for pkg deps Changes in version 0.1.0.6 (2021-06-29) - add barcode as identifiers and store identifiers within split_SE_components Changes in version 0.1.0.5 (2021-06-25) - update the logic for CI/CD (repos fetching is now handled with technical user) Changes in version 0.1.0.4 (2021-06-18) - add concentration and template as additional identifiers Changes in version 0.1.0.3 (2021-06-21) - refactor logisticFit with error handling Changes in version 0.1.0.2 (2021-06-18) - remove deprecated functions - switch from getMetadata to split_SE_components - refactor df_to_bm_assay Changes in version 0.1.0.1 (2021-06-02) - upgrade validate_SE by checking if rowData and colData do not have empty strings - isolate flatten function Changes in version 0.1.0.0 (2021-06-02) - release 1.0.0 Changes in version 0.0.0.49 (2021-06-02) - fix bug with merging flatten assays Changes in version 0.0.0.48 (2021-05-24) - refactor validate_SE function Changes in version 0.0.0.47 (2021-05-18) - add merge_SE function Changes in version 0.0.0.46 (2021-05-18) - fix typo in SE validator function Changes in version 0.0.0.45 (2021-05-18) - add SE validator function Changes in version 0.0.0.44 (2021-05-13) - refactor prettify_flat_metrics function Changes in version 0.0.0.43 (2021-04-30) - remove Metrics_rownames during flattening data.frame/data.table Changes in version 0.0.0.42 (2021-04-29) - add prettify_flat_metrics function Changes in version 0.0.0.41 (2021-04-29) - bugfix flattening data.tables Changes in version 0.0.0.40 (2021-04-29) - bugfix data.table merge in convert_se_assay_ref_to_dt Changes in version 0.0.0.39 (2021-04-27) - add support for flattening data.tables Changes in version 0.0.0.38 (2021-04-21) - switch from processing_metadata to .internal Changes in version 0.0.0.37 (2021-04-20) - add support for getting and setting processing info metadata Changes in version 0.0.0.36 (2021-04-19) - sort BumpyMatrix created from dt Changes in version 0.0.0.35 (2021-04-14) - revert metric arguments in 'convert_se_assay_to_dt' Changes in version 0.0.0.34 (2021-04-09) - add support for getting and setting fit parameter metadata Changes in version 0.0.0.33 (2021-04-07) - standardize metric header names Changes in version 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 Changes in version 0.0.0.31 (2021-03-30) - add support for getting and setting metadata on the SummarizedExperiment object Changes in version 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 Changes in version 0.0.0.29 (2021-03-23) - remove positional naming dependence on assay_to_dt for (merge_metrics = TRUE) argument Changes in version 0.0.0.28 (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 0.0.0.27 (2021-03-09) - update .estimate_xc50 and add tests Changes in version 0.0.0.26 (2021-03-04) - fix bug with wrong class for S3 methods in convert_assay_data_to_dt - update the documentation Changes in version 0.0.0.25 (2021-03-02) - fix bug with missing class in assert for matrix Changes in version 0.0.0.24 (2021-02-10) - modify fit_curves to take in flexible curve_type(s) - clean-up assay_to_dt Changes in version 0.0.0.23 (2021-02-04) - added linter Changes in version 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 Changes in version 0.0.0.21 (2021-01-26) - allow for DFrame as input Changes in version 0.0.0.20 (2021-01-26) - 's/BumpyMatrix::splitToBumpyMatrix/BumpyMatrix::splitAsBumpyMatrix/' Changes in version 0.0.0.19 (2021-01-20) - refactor RVGRfits and rename to fit_curves - make logisticFit function independent of curve_type Changes in version 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 Changes in version 0.0.0.15 (2020-12-14) - refactor get_identifiers and get_headers to be settable and cached Changes in version 0.0.0.14 (2020-12-14) - totally, finally, and unscrupulously remove dplyr package from gDRutils - replace IC by RV Changes in version 0.0.0.13 (2020-10-12) - add CI Changes in version 0.0.0.12 (2020-10-09) - fix assay_to_df Changes in version 0.0.0.11 (2020-10-09) - update namespaces Changes in version 0.0.0.10 (2020-10-05) - minor refactor Changes in version 0.0.0.9 (2020-09-14) - add small fixes for assays with empty DataFrame Changes in version 0.0.0.8 (2020-09-02) - update logic as per new db model Changes in version 0.0.0.7 (2020-08-07) - update variable names as per new db model Changes in version 0.0.0.6 (2020-07-02) - import pipes from magrittr Changes in version 0.0.0.4 (2020-06-10) - including the masked field to be able to remove the masked data from averages