Changes in version 2024-10-24 (2024-10-24) - split and refactor annotation functions Changes in version 2024-10-21 (2024-10-21) - add support for reprocessing data with old data model Changes in version 2024-09-30 (2024-09-30) - handle properly additional perturbations to get rid of creating additional columns that can't be hangle properly by the app Changes in version 2024-08-21 (2024-08-21) - identify additional perturbations hidden in the secondary drug Changes in version 2024-08-19 (2024-08-19) - utilize calc_sd function Changes in version 2024-08-09 (2024-08-09) - fix issue with wrong mapping of Day0 data Changes in version 2024-08-08 (2024-08-08) - fix issue with mapping overrides untreated controls Changes in version 2024-08-05 (2024-08-05) - fix issue with non-avearaged concentration data Changes in version 2024-07-23 (2024-07-23) - fix issue with providing empty nested_confounder Changes in version 2024-07-17 (2024-07-17) - allow using custom functions for calculating HSA and Bliss scores for combination data Changes in version 2024-07-15 (2024-07-15) - refactor logic for calculating standard deviation for single values Changes in version 2024-07-10 (2024-07-10) - update unit tests Changes in version 2024-06-04 (2024-06-04) - switch to get_supported_experiments Changes in version 2024-05-27 (2024-05-27) - synchronize Bioconductor and GitHub versioning Changes in version 2024-05-16 (2024-05-16) - move define_matrix_grid_positions and round_concentration functions to gDRutils package Changes in version 2024-05-13 (2024-05-13) - add functions for retrieving annotation data from input dt Changes in version 2024-05-08 (2024-05-08) - fix typo Changes in version 2024-04-23 (2024-04-23) - add vignette with documentation for data annotation Changes in version 2024-04-22 (2024-04-22) - add support for external annotation specified in the env var Changes in version 2024-03-26 (2024-03-26) - fix bug with converting mae into raw_data Changes in version 2024-03-15 (2024-03-15) - remove unstable tests Changes in version 2024-03-14 (2024-03-14) - cleanup package Changes in version 2024-03-12 (2024-03-12) - update function description Changes in version 2024-02-26 (2024-02-26) - improve pkgdown site - improved references - valid NEWS.md Changes in version 2024-02-14 (2024-02-14) - fix issue with retrieving unique records from mix of control and treated samples - make documentation compatible with pkdgdown - rename 'matches' to 'grr_matches' Changes in version 2024-02-12 (2024-02-12) - fix unit tests for GRAN Changes in version 2024-02-07 (2024-02-07) - simplify logic of assays for combination data - rename matrix into combination Changes in version 2024-02-06 (2024-02-06) - add support for internal source of annotation - fix bug with converting standardize MAE into raw data Changes in version 2024-02-05 (2024-02-05) - add vignette for a data model Changes in version 2024-02-01 (2024-02-01) - update wrappers for co-dilution data Changes in version 2024-01-22 (2024-01-22) - add new description fields Changes in version 2024-01-04 (2024-01-04) - improve logic for normalization and identification of single-agent and matrix data with Drug3 Changes in version 2023-12-15 (2023-12-15) - fix issue with wrong assignment of untreated records Changes in version 2023-11-22 (2023-11-22) - sync master with devel branch - add support for unifying duplicates in combo matrix data - 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 2023-10-17 (2023-10-17) - adjust NEWS to Bioc format Changes in version 2023-10-05 (2023-10-05) - bump version of gDRtestData - fix bug with merging controls in triple combo with additional perturbations Changes in version 2023-09-25 (2023-09-25) - add support for adding custom annotations inside input files - improve the performance - fix bug with subsetting wrong combo matrix value Changes in version 2023-09-19 (2023-09-19) - extend the logic for matching missing controls Changes in version 2023-09-12 (2023-09-12) - set Drug3 as an official tertiary drug in the experiment Changes in version 2023-09-04 (2023-09-04) - fill NA by average values when there is no match with plate Changes in version 2023-09-01 (2023-09-01) - fill NA during aggregation of ref and trt data with mean Changes in version 2023-08-17 (2023-08-17) - fix issue with missing subsetting Day0 data Changes in version 2023-08-16 (2023-08-16) - update logic for supporting manifest and template files sharing the same column Changes in version 2023-08-10 (2023-08-10) - update annotation column names for cell line annotation as per changes in the gDRutils Changes in version 2023-07-25 (2023-07-25) - extend logic for supporting cols with dash, e.g. additional perturbations with "-" Changes in version 2023-07-19 (2023-07-19) - update the logic for handling warnings in the pipeline Changes in version 2023-07-13 (2023-07-13) - fix issue with wrong merging of data.tables without nested confounders Changes in version 2023-07-07 (2023-07-07) - add information about source type for cases without metric data - refactor the logic for splitting raw data from metadata - get rid of iterative approach Changes in version 2023-07-05 (2023-07-05) - update logic for parallel computing Changes in version 2023-06-29 (2023-06-29) - optimize unit tests - remove backward compatibility for old data model Changes in version 2023-06-27 (2023-06-27) - fix bug with missing rownames in normalized assay Changes in version 2023-06-19 (2023-06-19) - update logic for merging data.table objects Changes in version 2023-06-13 (2023-06-13) - replace order with data.table::setorder Changes in version 2023-06-09 (2023-06-09) - switch from merge to [[ for data.table objects Changes in version 2023-06-07 (2023-06-07) - switch from zoo::rollmean to data.table::frollmean Changes in version 2023-06-06 (2023-06-06) - switch from aggregate to data.table - replace reshape2 functions by functions from data.table Changes in version 2023-05-31 (2023-05-31) - fix managing of mixed types of raw data Changes in version 2023-05-29 (2023-05-29) - fix bug with subsetting data for calculating isobologram Changes in version 2023-05-22 (2023-05-22) - format the vignette with BiocStyle Changes in version 2023-05-16 (2023-05-16) - fix related with data.table Changes in version 2023-05-15 (2023-05-15) - rename excess to x to unify colnames in assay data Changes in version 2023-05-10 (2023-05-10) - refactor normalization_types in combo-specific assays Changes in version 2023-05-09 (2023-05-09) - utilize gDRutils::apply_bumpy_function in fit_SE Changes in version 2023-05-05 (2023-05-05) - fix bug with swapping untreated/vehicle values Changes in version 2023-05-04 (2023-05-04) - fix bug with data.table Changes in version 2023-04-21 (2023-04-21) - utilize gDRutils::apply_bumpy_function in average_SE Changes in version 2023-04-20 (2023-04-20) - switch to OSI license Changes in version 2023-04-19 (2023-04-19) - fix bug with replacing vehicle to untreated values - moved wrapper fuctions from gDRtestData Changes in version 2023-04-18 (2023-04-18) - update dependencies - add fix for bioc-devel - correct sorting in merge test Changes in version 2023-04-17 (2023-04-17) - fix namespacing issue in examples - add R 4.2 as dependency - fix examples for normalize_SE Changes in version 2023-04-12 (2023-04-12) - add logic for retrieving raw data from assay data Changes in version 2023-04-07 (2023-04-07) - update maintainer Changes in version 2023-04-04 (2023-04-04) - bugfix for the logic in 'cleanup_metadata' Changes in version 2023-03-24 (2023-03-24) - make the package Bioc-compatible Changes in version 2023-03-21 (2023-03-21) - improve performance of 'map_df' with refactored logic for exact matches Changes in version 2023-03-15 (2023-03-15) - refactor pipeline Changes in version 2023-03-09 (2023-03-09) - address co-treatment fit by using the matrix data type instead Changes in version 2023-03-07 (2023-03-07) - add support for splitting normalization types Changes in version 2023-03-06 (2023-03-06) - improve logic in functions used to generate isobolograms' data - remove obsolete code Changes in version 2023-02-21 (2023-02-21) - add support for partial pipeline runs Changes in version 2023-02-10 (2023-02-10) - update path to annotation data - clean-up code Changes in version 2023-01-13 (2023-01-13) - clean-up code Changes in version 2023-01-12 (2023-01-12) - refactor mapping function to properly handle drug3 Changes in version 2022-12-16 (2022-12-16) - replace parallelize function with gDRutils::loop Changes in version 2022-12-15 (2022-12-15) - add assert for vehicle values in input data in runDrugResponseProcessingPipeline Changes in version 2022-12-14 (2022-12-14) - fix error-handling if conditions in average_SE Changes in version 2022-11-07 (2022-11-07) - fix invalid encapsulation in tests Changes in version 2022-10-18 (2022-10-18) - add missing namespacing Changes in version 2022-10-10 (2022-10-10) - add support for setting number of cores for BiocParallel based on the env variable Changes in version 2022-10-07 (2022-10-07) - remove global parameters for BiocParallel Changes in version 2022-09-29 (2022-09-29) - change the logic for using cores in BiocParallel Changes in version 2022-09-27 (2022-09-27) - update the logic for parallel computing Changes in version 2022-08-17 (2022-08-17) - update the logic for default nested_confounders in create_SE function Changes in version 2022-07-08 (2022-07-08) - refactor create_SE to support reverse single-agent data Changes in version 2022-06-02 (2022-06-02) - release 1.3.0 Changes in version 2022-05-30 (2022-05-30) - add missing namespace for get_env_identifiers Changes in version 2022-05-09 (2022-05-09) - replace NA by 0 in Concentration loaded in manifest file Changes in version 2022-05-06 (2022-05-06) - switch from data.table to data.frame in add_annotation* functions Changes in version 2022-04-12 (2022-04-12) - update function for adding unknown cell line annotations - update logic for using nested confounders - remove grr from dependencies Changes in version 2022-04-07 (2022-04-07) - get rid of gDRwrapper Changes in version 2022-03-30 (2022-03-30) - add support for additional barcode identifiers Changes in version 2022-03-18 (2022-03-18) - fix documentation in calculate_matrix_metric Changes in version 2022-03-17 (2022-03-17) - switch from catchr to purrr Changes in version 2022-03-02 (2022-03-02) - fix mapping reference values of inverted treatments - remove duplication of single-agent data Changes in version 2022-02-17 (2022-02-17) - wrap SE into MAE on the level of runDrugResponseProcessingPipeline Changes in version 2022-02-14 (2022-02-14) - change identifier drugname to drug_name Changes in version 2022-02-09 (2022-02-09) - switch from gDRinternal to gDRinternalData for internal annotations Changes in version 2022-02-08 (2022-02-08) - issue with subsetting by list in R 4.2.0 Changes in version 2022-02-02 (2022-02-02) - unlist output of intersect as per R 4.2.0 Changes in version 2022-01-31 (2022-01-31) - align version criteria between dependencies.yaml and DESCRIPTION package versions Changes in version 2022-01-25 (2022-01-25) - standardize/improve CI Changes in version 2022-01-24 (2022-01-24) - switch from cores variable to detect_cores- function - fix wrong type of NUM_CORES env variable Changes in version 2022-01-03 (2022-01-03) - speed-up functions for mapping treated and untreated cases Changes in version 2021-12-30 (2021-12-30) - fix linter issues Changes in version 2021-12-14 (2021-12-14) - use parallel computing as an alternative for for loops Changes in version 2021-12-07 (2021-12-07) - update annotation script as per new csv annotation files - detect co-trt data and treat them as single-agent Changes in version 2021-11-08 (2021-11-08) - set excess = NA for single-agent Changes in version 2021-10-29 (2021-10-29) - solve rounding issues - add new bliss metric Changes in version 2021-10-25 (2021-10-25) - refactor isobolograms - move p_trt_keys to the proper place Changes in version 2021-10-20 (2021-10-20) - add support for masked data in fit_SE.combinations.R Changes in version 2021-10-14 (2021-10-14) - address issues in creating the SE for combo matrix experiments Changes in version 2021-10-13 (2021-10-13) - refactor the logic for calculation Loewe when there is no Concentration == 0 Changes in version 2021-10-12 (2021-10-12) - refactor the logic for combo data Changes in version 2021-09-27 (2021-09-27) - updated normalization_types in 'calculate_combo_matrix' and 'fit_SE' Changes in version 2021-09-21 (2021-09-21) - calculate_GR_value by removing cl_name param Changes in version 2021-08-25 (2021-08-25) - fix but with missing nested_identifiers variables for creating DataFrame for masked values Changes in version 2021-08-04 (2021-08-04) - refactor reading annotations and add default parameters Changes in version 2021-07-30 (2021-07-30) - fix bug for nested_confounders not present in ref_df Changes in version 2021-07-27 (2021-07-27) - add support for nested_identifiers and nested_confounders Changes in version 2021-07-23 (2021-07-23) - remove obsolete dependencies from DESCRIPTION:Imports Changes in version 2021-07-01 (2021-07-01) - function for testing synthetic data Changes in version 2021-06-25 (2021-06-25) - move functions for importing template files to gDRimport package Changes in version 2021-06-23 (2021-06-23) - add linter - remove obsolete functions from test.utils.R Changes in version 2021-06-22 (2021-06-22) - move importing functions to gDRimport package Changes in version 2021-06-14 (2021-06-14) - add unit tests for synthetic data - remove deprecated functions and unit tests - update namespace for 'metadata- ' Changes in version 2021-06-10 (2021-06-10) - change package name - gDR => gDRcore Changes in version 2021-06-04 (2021-06-04) - export/update docs for 'standardize_record_values' Changes in version 2021-06-02 (2021-06-02) - release 1.0.0 Changes in version 2021-04-29 (2021-04-29) - remove all the gDRinternal-related files Changes in version 2021-04-27 (2021-04-27) - fix wrong argument name in fit_curves Changes in version 2021-04-23 (2021-04-23) - ensure that dts in assay- se,"Averaged" are NULL when there are not treatments Changes in version 2021-04-20 (2021-04-20) - add processing info metadata to SE Changes in version 2021-04-14 (2021-04-14) - improve handling of nested_keys and override_controls Changes in version 2021-04-09 (2021-04-09) - get rid of sorting index columns in getMetaData Changes in version 2021-03-31 (2021-03-31) - move SE metadata getters and setters to gDRutils - fix a bug in map_df function Changes in version 2021-03-26 (2021-03-26) - refactor processing functions in create_SE2, normalize_SE2, average_SE2, and fit_SE2 and friends Changes in version 2021-02-22 (2021-02-22) - add drug_moa_2 to merged df Changes in version 2021-02-17 (2021-02-17) - fix a bug with adding annotation to codrugs Changes in version 2021-02-04 (2021-02-04) - add script for benchmarking [normalize/average/metrics]-SE functions Changes in version 2021-02-02 (2021-02-02) - fix unit tests - include discard keys info in getMetaData for rowData Changes in version 2021-01-29 (2021-01-29) - utilize refactored and renamed fitting function RVGRfit to fit_curves Changes in version 2021-01-27 (2021-01-27) - export some functions for use in gDRutils Changes in version 2021-01-20 (2021-01-20) - move df_to_assay and df_to_bm_assay to gDRutils Changes in version 2021-01-18 (2021-01-18) - updated rowData and colData in SE with additional columns Changes in version 2021-01-14 (2021-01-14) - update positional header calls to explicit identifier calls - minor changes to comply with gDRstyle - minor changes to use identifiers over hard coded DrugName requirements Changes in version 2021-01-12 (2021-01-12) - update scripts related to annotation of drugs and cell lines Changes in version 2021-01-05 (2021-01-05) - anonymize test data Changes in version 2020-12-24 (2020-12-24) - switch from GeneDataScreenR to gDRinternal from QCS to gDR functions Changes in version 2020-12-22 (2020-12-22) - make createSE returning assays as 'BumpyMatrix' objects - previously 'matrix' objects only - add df_to_bm_assay function - returning BumpyMatrix object from raw experiment data - add initial tests for createSE function Changes in version 2020-12-21 (2020-12-21) - minor clean-up Changes in version 2020-12-15 (2020-12-15) - remove dplyr - use the latest version of gDRutils Changes in version 2020-12-07 (2020-12-07) - error messages Changes in version 2020-12-02 (2020-12-02) - refactor analyze_data.R with taking account codilution combo Changes in version 2020-11-24 (2020-11-24) - bug with reading raw data Changes in version 2020-11-08 (2020-11-08) - clean-up repository from duplicated functions Changes in version 2020-11-06 (2020-11-06) - switch to R 4.0 Changes in version 2020-10-01 (2020-10-01) - bugs in function for metrics calculation as per QCS dataset - QCS data - scripts for processing and pushing QCS data on Rosalind Changes in version 2020-09-29 (2020-09-29) - updated README.md Changes in version 2020-09-22 (2020-09-22) - bug in update_experiment_metadata Changes in version 2020-09-03 (2020-09-03) - logic as per new db model Changes in version 2020-08-26 (2020-08-26) - RDS files for the other GDS data - GDS5, GDS6, GDS7 Changes in version 2020-08-03 (2020-08-03) - support an import of single agent data from GDS - including the masked field to be able to remove the masked data from averages - add a function to annotate drug combinations - add_codrug_group - update the tests that contained combination experiments accordingly. - add new tests for the GDS data - minor refactor to use the 'masked' column. If it is not part of the initial dataframe it is added automatically - and set to FALSE Changes in version 2020-07-29 (2020-07-29) - fixed issue in update_experiment_metadata.R - unit test for update_experiment_metadata.R Changes in version 2020-07-14 (2020-07-14) - function for updating metadata in SE - dependencies: kcloak, gDRwrapper Changes in version 2020-07-08 (2020-07-08) - dependencies