NEWS

---

gDRcore 2024-11-15 (2024-11-15)

• fix melt in annotation function to fix Bioc error

gDRcore 2024-11-05 (2024-11-05)

• synchronize Bioconductor and GitHub versioning

gDRcore 2024-10-30 (2024-10-30)

• hot fix for annotation colnames of cell lines

gDRcore 2024-10-24 (2024-10-24)

• split and refactor annotation functions

gDRcore 2024-10-21 (2024-10-21)

• add support for reprocessing data with old data model

gDRcore 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

gDRcore 2024-08-21 (2024-08-21)

• identify additional perturbations hidden in the secondary drug

gDRcore 2024-08-19 (2024-08-19)

• utilize calc_sd function

gDRcore 2024-08-09 (2024-08-09)

• fix issue with wrong mapping of Day0 data

gDRcore 2024-08-08 (2024-08-08)

• fix issue with mapping overrides untreated controls

gDRcore 2024-08-05 (2024-08-05)

• fix issue with non-avearaged concentration data

gDRcore 2024-07-23 (2024-07-23)

• fix issue with providing empty nested_confounder

gDRcore 2024-07-17 (2024-07-17)

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

gDRcore 2024-07-15 (2024-07-15)

• refactor logic for calculating standard deviation for single values

gDRcore 2024-07-10 (2024-07-10)

• update unit tests

gDRcore 2024-06-04 (2024-06-04)

• switch to get_supported_experiments

gDRcore 2024-05-27 (2024-05-27)

• synchronize Bioconductor and GitHub versioning

gDRcore 2024-05-16 (2024-05-16)

• move define_matrix_grid_positions and round_concentration functions to gDRutils package

gDRcore 2024-05-13 (2024-05-13)

• add functions for retrieving annotation data from input dt

gDRcore 2024-05-08 (2024-05-08)

• fix typo

gDRcore 2024-04-23 (2024-04-23)

• add vignette with documentation for data annotation

gDRcore 2024-04-22 (2024-04-22)

• add support for external annotation specified in the env var

gDRcore 2024-03-26 (2024-03-26)

• fix bug with converting mae into raw_data

gDRcore 2024-03-15 (2024-03-15)

• remove unstable tests

gDRcore 2024-03-14 (2024-03-14)

• cleanup package

gDRcore 2024-03-12 (2024-03-12)

• update function description

gDRcore 2024-02-26 (2024-02-26)

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

gDRcore 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'

gDRcore 2024-02-12 (2024-02-12)

• fix unit tests for GRAN

gDRcore 2024-02-07 (2024-02-07)

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

gDRcore 2024-02-06 (2024-02-06)

• add support for internal source of annotation

• fix bug with converting standardize MAE into raw data

gDRcore 2024-02-05 (2024-02-05)

• add vignette for a data model

gDRcore 2024-02-01 (2024-02-01)

• update wrappers for co-dilution data

gDRcore 2024-01-22 (2024-01-22)

• add new description fields

gDRcore 2024-01-04 (2024-01-04)

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

gDRcore 2023-12-15 (2023-12-15)

• fix issue with wrong assignment of untreated records

gDRcore 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

gDRcore 2023-10-24 (2023-10-24)

• release Bioc 3.18

• prerelease Bioc 3.18

gDRcore 2023-10-17 (2023-10-17)

• adjust NEWS to Bioc format

gDRcore 2023-10-05 (2023-10-05)

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

gDRcore 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

gDRcore 2023-09-19 (2023-09-19)

• extend the logic for matching missing controls

gDRcore 2023-09-12 (2023-09-12)

• set Drug3 as an official tertiary drug in the experiment

gDRcore 2023-09-04 (2023-09-04)

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

gDRcore 2023-09-01 (2023-09-01)

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

gDRcore 2023-08-17 (2023-08-17)

• fix issue with missing subsetting Day0 data

gDRcore 2023-08-16 (2023-08-16)

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

gDRcore 2023-08-10 (2023-08-10)

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

gDRcore 2023-07-25 (2023-07-25)

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

gDRcore 2023-07-19 (2023-07-19)

• update the logic for handling warnings in the pipeline

gDRcore 2023-07-13 (2023-07-13)

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

gDRcore 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

gDRcore 2023-07-05 (2023-07-05)

• update logic for parallel computing

gDRcore 2023-06-29 (2023-06-29)

• optimize unit tests

• remove backward compatibility for old data model

gDRcore 2023-06-27 (2023-06-27)

• fix bug with missing rownames in normalized assay

gDRcore 2023-06-19 (2023-06-19)

• update logic for merging data.table objects

gDRcore 2023-06-13 (2023-06-13)

• replace order with data.table::setorder

gDRcore 2023-06-09 (2023-06-09)

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

gDRcore 2023-06-07 (2023-06-07)

• switch from zoo::rollmean to data.table::frollmean

gDRcore 2023-06-06 (2023-06-06)

• switch from aggregate to data.table

• replace reshape2 functions by functions from data.table

gDRcore 2023-05-31 (2023-05-31)

• fix managing of mixed types of raw data

gDRcore 2023-05-29 (2023-05-29)

• fix bug with subsetting data for calculating isobologram

gDRcore 2023-05-22 (2023-05-22)

• format the vignette with BiocStyle

gDRcore 2023-05-16 (2023-05-16)

• fix related with data.table

gDRcore 2023-05-15 (2023-05-15)

• rename excess to x to unify colnames in assay data

gDRcore 2023-05-10 (2023-05-10)

• refactor normalization_types in combo-specific assays

gDRcore 2023-05-09 (2023-05-09)

• utilize gDRutils::apply_bumpy_function in fit_SE

gDRcore 2023-05-05 (2023-05-05)

• fix bug with swapping untreated/vehicle values

gDRcore 2023-05-04 (2023-05-04)

• fix bug with data.table

gDRcore 2023-04-21 (2023-04-21)

• utilize gDRutils::apply_bumpy_function in average_SE

gDRcore 2023-04-20 (2023-04-20)

• switch to OSI license

gDRcore 2023-04-19 (2023-04-19)

• fix bug with replacing vehicle to untreated values

• moved wrapper fuctions from gDRtestData

gDRcore 2023-04-18 (2023-04-18)

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

gDRcore 2023-04-17 (2023-04-17)

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

gDRcore 2023-04-12 (2023-04-12)

• add logic for retrieving raw data from assay data

gDRcore 2023-04-07 (2023-04-07)

• update maintainer

gDRcore 2023-04-04 (2023-04-04)

• bugfix for the logic in 'cleanup_metadata'

gDRcore 2023-03-24 (2023-03-24)

• make the package Bioc-compatible

gDRcore 2023-03-21 (2023-03-21)

• improve performance of 'map_df' with refactored logic for exact matches

gDRcore 2023-03-15 (2023-03-15)

• refactor pipeline

gDRcore 2023-03-09 (2023-03-09)

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

gDRcore 2023-03-07 (2023-03-07)

• add support for splitting normalization types

gDRcore 2023-03-06 (2023-03-06)

• improve logic in functions used to generate isobolograms' data

• remove obsolete code

gDRcore 2023-02-21 (2023-02-21)

• add support for partial pipeline runs

gDRcore 2023-02-10 (2023-02-10)

• update path to annotation data

• clean-up code

gDRcore 2023-01-13 (2023-01-13)

• clean-up code

gDRcore 2023-01-12 (2023-01-12)

• refactor mapping function to properly handle drug3

gDRcore 2022-12-16 (2022-12-16)

• replace parallelize function with gDRutils::loop

gDRcore 2022-12-15 (2022-12-15)

• add assert for vehicle values in input data in runDrugResponseProcessingPipeline

gDRcore 2022-12-14 (2022-12-14)

• fix error-handling if conditions in average_SE

gDRcore 2022-11-07 (2022-11-07)

• fix invalid encapsulation in tests

gDRcore 2022-10-18 (2022-10-18)

• add missing namespacing

gDRcore 2022-10-10 (2022-10-10)

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

gDRcore 2022-10-07 (2022-10-07)

• remove global parameters for BiocParallel

gDRcore 2022-09-29 (2022-09-29)

• change the logic for using cores in BiocParallel

gDRcore 2022-09-27 (2022-09-27)

• update the logic for parallel computing

gDRcore 2022-08-17 (2022-08-17)

• update the logic for default nested_confounders in create_SE function

gDRcore 2022-07-08 (2022-07-08)

• refactor create_SE to support reverse single-agent data

gDRcore 2022-06-02 (2022-06-02)

• release 1.3.0

gDRcore 2022-05-30 (2022-05-30)

• add missing namespace for get_env_identifiers

gDRcore 2022-05-09 (2022-05-09)

• replace NA by 0 in Concentration loaded in manifest file

gDRcore 2022-05-06 (2022-05-06)

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

gDRcore 2022-04-12 (2022-04-12)

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

gDRcore 2022-04-07 (2022-04-07)

• get rid of gDRwrapper

gDRcore 2022-03-30 (2022-03-30)

• add support for additional barcode identifiers

gDRcore 2022-03-18 (2022-03-18)

• fix documentation in calculate_matrix_metric

gDRcore 2022-03-17 (2022-03-17)

• switch from catchr to purrr

gDRcore 2022-03-02 (2022-03-02)

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

gDRcore 2022-02-17 (2022-02-17)

• wrap SE into MAE on the level of runDrugResponseProcessingPipeline

gDRcore 2022-02-14 (2022-02-14)

• change identifier drugname to drug_name

gDRcore 2022-02-09 (2022-02-09)

• switch from gDRinternal to gDRinternalData for internal annotations

gDRcore 2022-02-08 (2022-02-08)

• issue with subsetting by list in R 4.2.0

gDRcore 2022-02-02 (2022-02-02)

• unlist output of intersect as per R 4.2.0

gDRcore 2022-01-31 (2022-01-31)

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

gDRcore 2022-01-25 (2022-01-25)

• standardize/improve CI

gDRcore 2022-01-24 (2022-01-24)

• switch from cores variable to detect_cores- function

• fix wrong type of NUM_CORES env variable

gDRcore 2022-01-03 (2022-01-03)

• speed-up functions for mapping treated and untreated cases

gDRcore 2021-12-30 (2021-12-30)

• fix linter issues

gDRcore 2021-12-14 (2021-12-14)

• use parallel computing as an alternative for for loops

gDRcore 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

gDRcore 2021-11-08 (2021-11-08)

• set excess = NA for single-agent

gDRcore 2021-10-29 (2021-10-29)

• solve rounding issues
• add new bliss metric

gDRcore 2021-10-25 (2021-10-25)

• refactor isobolograms

• move p_trt_keys to the proper place

gDRcore 2021-10-20 (2021-10-20)

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

gDRcore 2021-10-14 (2021-10-14)

• address issues in creating the SE for combo matrix experiments

gDRcore 2021-10-13 (2021-10-13)

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

gDRcore 2021-10-12 (2021-10-12)

• refactor the logic for combo data

gDRcore 2021-09-27 (2021-09-27)

• updated normalization_types in 'calculate_combo_matrix' and 'fit_SE'

gDRcore 2021-09-21 (2021-09-21)

• calculate_GR_value by removing cl_name param

gDRcore 2021-08-25 (2021-08-25)

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

gDRcore 2021-08-04 (2021-08-04)

• refactor reading annotations and add default parameters

gDRcore 2021-07-30 (2021-07-30)

• fix bug for nested_confounders not present in ref_df

gDRcore 2021-07-27 (2021-07-27)

• add support for nested_identifiers and nested_confounders

gDRcore 2021-07-23 (2021-07-23)

• remove obsolete dependencies from DESCRIPTION:Imports

gDRcore 2021-07-01 (2021-07-01)

• function for testing synthetic data

gDRcore 2021-06-25 (2021-06-25)

• move functions for importing template files to gDRimport package

gDRcore 2021-06-23 (2021-06-23)

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

gDRcore 2021-06-22 (2021-06-22)

• move importing functions to gDRimport package

gDRcore 2021-06-14 (2021-06-14)

• add unit tests for synthetic data

• remove deprecated functions and unit tests

• update namespace for 'metadata- '

gDRcore 2021-06-10 (2021-06-10)

• change package name - gDR => gDRcore

gDRcore 2021-06-04 (2021-06-04)

• export/update docs for 'standardize_record_values'

gDRcore 2021-06-02 (2021-06-02)

• release 1.0.0

gDRcore 2021-04-29 (2021-04-29)

• remove all the gDRinternal-related files

gDRcore 2021-04-27 (2021-04-27)

• fix wrong argument name in fit_curves

gDRcore 2021-04-23 (2021-04-23)

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

gDRcore 2021-04-20 (2021-04-20)

• add processing info metadata to SE

gDRcore 2021-04-14 (2021-04-14)

• improve handling of nested_keys and override_controls

gDRcore 2021-04-09 (2021-04-09)

• get rid of sorting index columns in getMetaData

gDRcore 2021-03-31 (2021-03-31)

• move SE metadata getters and setters to gDRutils

• fix a bug in map_df function

gDRcore 2021-03-26 (2021-03-26)

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

gDRcore 2021-02-22 (2021-02-22)

• add drug_moa_2 to merged df

gDRcore 2021-02-17 (2021-02-17)

• fix a bug with adding annotation to codrugs

gDRcore 2021-02-04 (2021-02-04)

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

gDRcore 2021-02-02 (2021-02-02)

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

gDRcore 2021-01-29 (2021-01-29)

• utilize refactored and renamed fitting function RVGRfit to fit_curves

gDRcore 2021-01-27 (2021-01-27)

• export some functions for use in gDRutils

gDRcore 2021-01-20 (2021-01-20)

• move df_to_assay and df_to_bm_assay to gDRutils

gDRcore 2021-01-18 (2021-01-18)

• updated rowData and colData in SE with additional columns

gDRcore 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

gDRcore 2021-01-12 (2021-01-12)

• update scripts related to annotation of drugs and cell lines

gDRcore 2021-01-05 (2021-01-05)

• anonymize test data

gDRcore 2020-12-24 (2020-12-24)

• switch from GeneDataScreenR to gDRinternal from QCS to gDR functions

gDRcore 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

gDRcore 2020-12-21 (2020-12-21)

• minor clean-up

gDRcore 2020-12-15 (2020-12-15)

• remove dplyr
• use the latest version of gDRutils

gDRcore 2020-12-07 (2020-12-07)

• error messages

gDRcore 2020-12-02 (2020-12-02)

• refactor analyze_data.R with taking account codilution combo

gDRcore 2020-11-24 (2020-11-24)

• bug with reading raw data

gDRcore 2020-11-08 (2020-11-08)

• clean-up repository from duplicated functions

gDRcore 2020-11-06 (2020-11-06)

• switch to R 4.0

gDRcore 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

gDRcore 2020-09-29 (2020-09-29)

• updated README.md

gDRcore 2020-09-22 (2020-09-22)

• bug in update_experiment_metadata

gDRcore 2020-09-03 (2020-09-03)

• logic as per new db model

gDRcore 2020-08-26 (2020-08-26)

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

gDRcore 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

gDRcore 2020-07-29 (2020-07-29)

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

gDRcore 2020-07-14 (2020-07-14)

• function for updating metadata in SE

• dependencies: kcloak, gDRwrapper

gDRcore 2020-07-08 (2020-07-08)

• dependencies