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Changelog

Source: NEWS.md

gDRcore 1.5.2 - 2024-11-15

  • fix melt in annotation function to fix Bioc error

gDRcore 1.5.1 - 2024-11-05

  • synchronize Bioconductor and GitHub versioning

gDRcore 1.3.15 - 2024-10-30

  • hot fix for annotation colnames of cell lines

gDRcore 1.3.14 - 2024-10-24

  • split and refactor annotation functions

gDRcore 1.3.13 - 2024-10-21

  • add support for reprocessing data with old data model

gDRcore 1.3.12 - 2024-09-30

  • handle properly additional perturbations to get rid of creating additional columns that can’t be hangle properly by the app

gDRcore 1.3.11 - 2024-08-21

  • identify additional perturbations hidden in the secondary drug

gDRcore 1.3.10 - 2024-08-19

  • utilize calc_sd function

gDRcore 1.3.9 - 2024-08-09

  • fix issue with wrong mapping of Day0 data

gDRcore 1.3.8 - 2024-08-08

  • fix issue with mapping overrides untreated controls

gDRcore 1.3.7 - 2024-08-05

  • fix issue with non-avearaged concentration data

gDRcore 1.3.6 - 2024-07-23

  • fix issue with providing empty nested_confounder

gDRcore 1.3.5 - 2024-07-17

  • allow using custom functions for calculating HSA and Bliss scores for combination data

gDRcore 1.3.4 - 2024-07-15

  • refactor logic for calculating standard deviation for single values

gDRcore 1.3.3 - 2024-07-10

  • update unit tests

gDRcore 1.3.2 - 2024-06-04

  • switch to get_supported_experiments

gDRcore 1.3.1 - 2024-05-27

  • synchronize Bioconductor and GitHub versioning

gDRcore 1.1.22 - 2024-05-16

  • move define_matrix_grid_positions and round_concentration functions to gDRutils package

gDRcore 1.1.21 - 2024-05-13

  • add functions for retrieving annotation data from input dt

gDRcore 1.1.20 - 2024-05-08

  • fix typo

gDRcore 1.1.19 - 2024-04-23

  • add vignette with documentation for data annotation

gDRcore 1.1.18 - 2024-04-22

  • add support for external annotation specified in the env var

gDRcore 1.1.17 - 2024-03-26

  • fix bug with converting mae into raw_data

gDRcore 1.1.16 - 2024-03-15

  • remove unstable tests

gDRcore 1.1.15 - 2024-03-14

  • cleanup package

gDRcore 1.1.14 - 2024-03-12

  • update function description

gDRcore 1.1.13 - 2024-02-26

  • improve pkgdown site
    • improved references
    • valid NEWS.md

gDRcore 1.1.12 - 2024-02-14

  • fix issue with retrieving unique records from mix of control and treated samples

gDRcore 1.1.11 - 2024-02-14

  • make documentation compatible with pkdgdown
  • rename ‘matches’ to ‘grr_matches’

gDRcore 1.1.10 - 2024-02-12

  • fix unit tests for GRAN

gDRcore 1.1.9 - 2024-02-07

  • simplify logic of assays for combination data
  • rename matrix into combination

gDRcore 1.1.8 - 2024-02-06

  • add support for internal source of annotation

gDRcore 1.1.7 - 2024-02-06

  • fix bug with converting standardize MAE into raw data

gDRcore 1.1.6 - 2024-02-05

  • add vignette for a data model

gDRcore 1.1.5 - 2024-02-01

  • update wrappers for co-dilution data

gDRcore 1.1.4 - 2024-01-22

  • add new description fields

gDRcore 1.1.3 - 2024-01-04

  • improve logic for normalization and identification of single-agent and matrix data with Drug3

gDRcore 1.1.2 - 2023-12-15

  • fix issue with wrong assignment of untreated records

gDRcore 1.1.1 - 2023-11-22

  • sync master with devel branch
  • add support for unifying duplicates in combo matrix data
  • add “Treatment” as template identifier

gDRcore 1.1.0 - 2023-10-24

  • release Bioc 3.18

gDRcore 1.0.0 - 2023-10-24

  • prerelease Bioc 3.18

gDRcore 0.99.43 - 2023-10-17

  • adjust NEWS to Bioc format

gDRcore 0.99.42 - 2023-10-05

  • bump version of gDRtestData
  • fix bug with merging controls in triple combo with additional perturbations

gDRcore 0.99.41 - 2023-09-25

  • add support for adding custom annotations inside input files
  • improve the performance

gDRcore 0.99.40 - 2023-09-25

  • fix bug with subsetting wrong combo matrix value

gDRcore 0.99.39 - 2023-09-19

  • extend the logic for matching missing controls

gDRcore 0.99.38 - 2023-09-12

  • set Drug3 as an official tertiary drug in the experiment

gDRcore 0.99.37 - 2023-09-04

  • fill NA by average values when there is no match with plate

gDRcore 0.99.36 - 2023-09-01

  • fill NA during aggregation of ref and trt data with mean

gDRcore 0.99.35 - 2023-08-17

  • fix issue with missing subsetting Day0 data

gDRcore 0.99.34 - 2023-08-16

  • update logic for supporting manifest and template files sharing the same column

gDRcore 0.99.33 - 2023-08-10

  • update annotation column names for cell line annotation as per changes in the gDRutils

gDRcore 0.99.32 - 2023-07-25

  • extend logic for supporting cols with dash, e.g. additional perturbations with “-”

gDRcore 0.99.31 - 2023-07-19

  • update the logic for handling warnings in the pipeline

gDRcore 0.99.30 - 2023-07-13

  • fix issue with wrong merging of data.tables without nested confounders

gDRcore 0.99.29 - 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

gDRcore 0.99.28 - 2023-07-05

  • update logic for parallel computing

gDRcore 0.99.27 - 2023-06-29

  • optimize unit tests

gDRcore 0.99.26 - 2023-06-29

  • remove backward compatibility for old data model

gDRcore 0.99.25 - 2023-06-27

  • fix bug with missing rownames in normalized assay

gDRcore 0.99.24 - 2023-06-19

  • update logic for merging data.table objects

gDRcore 0.99.23 - 2023-06-13

gDRcore 0.99.22 - 2023-06-09

  • switch from merge to [[ for data.table objects

gDRcore 0.99.21 - 2023-06-06

  • switch from aggregate to data.table

gDRcore 0.99.20 - 2023-06-07

gDRcore 0.99.19 - 2023-06-06

  • replace reshape2 functions by functions from data.table

gDRcore 0.99.18 - 2023-05-31

  • fix managing of mixed types of raw data

gDRcore 0.99.17 - 2023-05-29

  • fix bug with subsetting data for calculating isobologram

gDRcore 0.99.16 - 2023-05-22

  • format the vignette with BiocStyle

gDRcore 0.99.15 - 2023-05-16

  • fix related with data.table

gDRcore 0.99.14 - 2023-05-15

  • rename excess to x to unify colnames in assay data

gDRcore 0.99.13 - 2023-05-10

  • refactor normalization_types in combo-specific assays

gDRcore 0.99.12 - 2023-05-09

gDRcore 0.99.11 - 2023-05-05

  • fix bug with swapping untreated/vehicle values

gDRcore 0.99.10 - 2023-05-04

  • fix bug with data.table

gDRcore 0.99.9 - 2023-04-21

gDRcore 0.99.8 - 2023-04-20

  • switch to OSI license

gDRcore 0.99.7 - 2023-04-19

  • fix bug with replacing vehicle to untreated values

gDRcore 0.99.6 - 2023-04-19

  • moved wrapper fuctions from gDRtestData

gDRcore 0.99.5 - 2023-04-18

  • update dependencies
  • add fix for bioc-devel - correct sorting in merge test

gDRcore 0.99.4 - 2023-04-17

  • fix namespacing issue in examples
  • add R 4.2 as dependency
  • fix examples for normalize_SE

gDRcore 0.99.3 - 2023-04-12

  • add logic for retrieving raw data from assay data

gDRcore 0.99.2 - 2023-04-07

  • update maintainer

gDRcore 0.99.1 - 2023-04-04

  • bugfix for the logic in ‘cleanup_metadata’

gDRcore 0.99.0 - 2023-03-24

  • make the package Bioc-compatible

gDRcore 0.1.3.22 - 2023-03-21

  • improve performance of ‘map_df’ with refactored logic for exact matches

gDRcore 0.1.3.21 - 2023-03-15

  • refactor pipeline

gDRcore 0.1.3.20 - 2023-03-09

  • address co-treatment fit by using the matrix data type instead

gDRcore 0.1.3.19 - 2023-03-07

  • add support for splitting normalization types

gDRcore 0.1.3.18 - 2023-03-06

  • improve logic in functions used to generate isobolograms’ data

gDRcore 0.1.3.17 - 2023-03-06

  • remove obsolete code

gDRcore 0.1.3.16 - 2023-02-21

  • add support for partial pipeline runs

gDRcore 0.1.3.15 - 2023-02-10

  • update path to annotation data

gDRcore 0.1.3.14 - 2023-02-10

  • clean-up code

gDRcore 0.1.3.13 - 2023-01-13

  • clean-up code

gDRcore 0.1.3.12 - 2023-01-12

  • refactor mapping function to properly handle drug3

gDRcore 0.1.3.11 - 2022-12-16

  • replace parallelize function with gDRutils::loop

gDRcore 0.1.3.10 - 2022-12-15

  • add assert for vehicle values in input data in runDrugResponseProcessingPipeline

gDRcore 0.1.3.9 - 2022-12-14

  • fix error-handling if conditions in average_SE

gDRcore 0.1.3.8 - 2022-11-07

  • fix invalid encapsulation in tests

gDRcore 0.1.3.7 - 2022-10-18

  • add missing namespacing

gDRcore 0.1.3.6 - 2022-10-10

  • add support for setting number of cores for BiocParallel based on the env variable

gDRcore 0.1.3.5 - 2022-10-07

  • remove global parameters for BiocParallel

gDRcore 0.1.3.4 - 2022-09-29

  • change the logic for using cores in BiocParallel

gDRcore 0.1.3.3 - 2022-09-27

  • update the logic for parallel computing

gDRcore 0.1.3.2 - 2022-08-17

  • update the logic for default nested_confounders in create_SE function

gDRcore 0.1.3.1 - 2022-07-08

  • refactor create_SE to support reverse single-agent data

gDRcore 0.1.3.0 - 2022-06-02

  • release 1.3.0

gDRcore 0.1.1.39 - 2022-05-30

  • add missing namespace for get_env_identifiers

gDRcore 0.1.1.38 - 2022-05-09

  • replace NA by 0 in Concentration loaded in manifest file

gDRcore 0.1.1.37 - 2022-05-06

  • switch from data.table to data.frame in add_annotation* functions

gDRcore 0.1.1.36 - 2022-04-12

  • update function for adding unknown cell line annotations
  • update logic for using nested confounders
  • remove grr from dependencies

gDRcore 0.1.1.35 - 2022-04-07

  • get rid of gDRwrapper

gDRcore 0.1.1.34 - 2022-03-30

  • add support for additional barcode identifiers

gDRcore 0.1.1.33 - 2022-03-18

  • fix documentation in calculate_matrix_metric

gDRcore 0.1.1.32 - 2022-03-17

  • switch from catchr to purrr

gDRcore 0.1.1.31 - 2022-03-02

  • fix mapping reference values of inverted treatments
  • remove duplication of single-agent data

gDRcore 0.1.1.30 - 2022-02-17

  • wrap SE into MAE on the level of runDrugResponseProcessingPipeline

gDRcore 0.1.1.29 - 2022-02-14

  • change identifier drugname to drug_name

gDRcore 0.1.1.28 - 2022-02-09

  • switch from gDRinternal to gDRinternalData for internal annotations

gDRcore 0.1.1.27 - 2022-02-08

  • issue with subsetting by list in R 4.2.0

gDRcore 0.1.1.26 - 2022-02-02

  • unlist output of intersect as per R 4.2.0

gDRcore 0.1.1.25 - 2022-01-31

  • align version criteria between dependencies.yaml and DESCRIPTION package versions

gDRcore 0.1.1.24 - 2022-01-25

  • standardize/improve CI

gDRcore 0.1.1.23 - 2022-01-24

  • switch from cores variable to detect_cores- function

gDRcore 0.1.1.22 - 2022-01-24

  • fix wrong type of NUM_CORES env variable

gDRcore 0.1.1.21 - 2022-01-03

  • speed-up functions for mapping treated and untreated cases

gDRcore 0.1.1.20 - 2021-12-30

  • fix linter issues

gDRcore 0.1.1.19 - 2021-12-14

  • use parallel computing as an alternative for for loops

gDRcore 0.1.1.18 - 2021-12-07

  • update annotation script as per new csv annotation files

gDRcore 0.1.1.17 - 2021-12-07

  • detect co-trt data and treat them as single-agent

gDRcore 0.1.1.16 - 2021-11-08

  • set excess = NA for single-agent

gDRcore 0.1.1.15 - 2021-10-29

  • solve rounding issues
  • add new bliss metric

gDRcore 0.1.1.14 - 2021-10-25

  • refactor isobolograms

gDRcore 0.1.1.13 - 2021-10-25

  • move p_trt_keys to the proper place

gDRcore 0.1.1.12 - 2021-10-20

  • add support for masked data in fit_SE.combinations.R

gDRcore 0.1.1.11 - 2021-10-14

  • address issues in creating the SE for combo matrix experiments

gDRcore 0.1.1.10 - 2021-10-13

  • refactor the logic for calculation Loewe when there is no Concentration == 0

gDRcore 0.1.1.9 - 2021-10-12

  • refactor the logic for combo data

gDRcore 0.1.1.8 - 2021-09-27

  • updated normalization_types in ‘calculate_combo_matrix’ and ‘fit_SE’

gDRcore 0.1.1.7 - 2021-09-21

  • calculate_GR_value by removing cl_name param

gDRcore 0.1.1.6 - 2021-08-25

  • fix but with missing nested_identifiers variables for creating DataFrame for masked values

gDRcore 0.1.1.5 - 2021-08-04

  • refactor reading annotations and add default parameters

gDRcore 0.1.1.4 - 2021-07-30

  • fix bug for nested_confounders not present in ref_df

gDRcore 0.1.1.3 - 2021-07-27

  • add support for nested_identifiers and nested_confounders

gDRcore 0.1.1.2 - 2021-07-23

  • remove obsolete dependencies from DESCRIPTION:Imports

gDRcore 0.1.0.9 - 2021-07-01

  • function for testing synthetic data

gDRcore 0.1.0.8 - 2021-06-25

  • move functions for importing template files to gDRimport package

gDRcore 0.1.0.7 - 2021-06-23

  • add linter
  • remove obsolete functions from test.utils.R

gDRcore 0.1.0.6 - 2021-06-22

  • move importing functions to gDRimport package

gDRcore 0.1.0.5 - 2021-06-14

  • add unit tests for synthetic data

gDRcore 0.1.0.4 - 2021-06-14

  • remove deprecated functions and unit tests

gDRcore 0.1.0.3 - 2021-06-14

  • update namespace for ‘metadata-’

gDRcore 0.1.0.2 - 2021-06-10

  • change package name - gDR => gDRcore

gDRcore 0.1.0.1 - 2021-06-04

  • export/update docs for ‘standardize_record_values’

gDRcore 0.1.0.0 - 2021-06-02

  • release 1.0.0

gDRcore 0.0.1.52 - 2021-04-29

  • remove all the gDRinternal-related files

gDRcore 0.0.1.51 - 2021-04-27

  • fix wrong argument name in fit_curves

gDRcore 0.0.1.50 - 2021-04-23

  • ensure that dts in assay- se,"Averaged" are NULL when there are not treatments

gDRcore 0.0.1.49 - 2021-04-20

  • add processing info metadata to SE

gDRcore 0.0.1.48 - 2021-04-14

  • improve handling of nested_keys and override_controls

gDRcore 0.0.1.47 - 2021-04-09

  • get rid of sorting index columns in getMetaData

gDRcore 0.0.1.46 - 2021-03-31

  • move SE metadata getters and setters to gDRutils

gDRcore 0.0.1.45 - 2021-03-31

  • fix a bug in map_df function

gDRcore 0.0.1.44 - 2021-03-26

  • refactor processing functions in create_SE2, normalize_SE2, average_SE2, and fit_SE2 and friends

gDRcore 0.0.1.43 - 2021-02-22

  • add drug_moa_2 to merged df

gDRcore 0.0.1.42 - 2021-02-17

  • fix a bug with adding annotation to codrugs

gDRcore 0.0.1.41 - 2021-02-04

  • add script for benchmarking [normalize/average/metrics]-SE functions

gDRcore 0.0.1.40 - 2021-02-02

  • fix unit tests
  • include discard keys info in getMetaData for rowData

gDRcore 0.0.1.39 - 2021-01-29

  • utilize refactored and renamed fitting function RVGRfit to fit_curves

gDRcore 0.0.1.38 - 2021-01-27

  • export some functions for use in gDRutils

gDRcore 0.0.1.37 - 2021-01-20

  • move df_to_assay and df_to_bm_assay to gDRutils

gDRcore 0.0.1.36 - 2021-01-18

  • updated rowData and colData in SE with additional columns

gDRcore 0.0.1.35 - 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

gDRcore 0.0.1.34 - 2021-01-12

  • update scripts related to annotation of drugs and cell lines

gDRcore 0.0.1.33 - 2021-01-05

  • anonymize test data

gDRcore 0.0.1.32 - 2020-12-24

  • switch from GeneDataScreenR to gDRinternal from QCS to gDR functions

gDRcore 0.0.1.31 - 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

gDRcore 0.0.1.30 - 2020-12-21

  • minor clean-up

gDRcore 0.0.1.29 - 2020-12-15

  • remove dplyr
  • use the latest version of gDRutils

gDRcore 0.0.1.28 - 2020-12-07

  • error messages

gDRcore 0.0.1.27 - 2020-12-02

  • refactor analyze_data.R with taking account codilution combo

gDRcore 0.0.1.26 - 2020-11-24

  • bug with reading raw data

gDRcore 0.0.1.25 - 2020-11-08

  • clean-up repository from duplicated functions

gDRcore 0.0.1.25 - 2020-11-06

  • switch to R 4.0

gDRcore 0.0.1.24 - 2020-10-01

  • bugs in function for metrics calculation as per QCS dataset
  • QCS data
  • scripts for processing and pushing QCS data on Rosalind

gDRcore 0.0.1.23 - 2020-09-29

  • updated README.md

gDRcore 0.0.1.22 - 2020-09-22

  • bug in update_experiment_metadata

gDRcore 0.0.1.21 - 2020-09-03

  • logic as per new db model

gDRcore 0.0.1.20 - 2020-08-26

  • RDS files for the other GDS data - GDS5, GDS6, GDS7

gDRcore 0.0.1.19 - 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

gDRcore 0.0.1.18 - 2020-07-29

  • fixed issue in update_experiment_metadata.R
  • unit test for update_experiment_metadata.R

gDRcore 0.0.1.17 - 2020-07-14

  • function for updating metadata in SE

gDRcore 0.0.1.16 - 2020-07-14

  • dependencies: kcloak, gDRwrapper

gDRcore 0.0.1.15 - 2020-07-08

  • dependencies