NEWS

---

gDRutils 2024-12-10 (2024-12-10)

• make split_SE_components working correctly for sa assay data, modified with avearge_biological_duplicates

gDRutils 2024-12-09 (2024-12-09)

• minor improvement in the logic of average_biological_replicates (new blacklisted column)

gDRutils 2024-12-02 (2024-12-02)

• refactor set_unique_* functions

gDRutils 2024-11-05 (2024-11-05)

• add get_env_var helper

• synchronize Bioconductor and GitHub versioning

gDRutils 2024-10-24 (2024-10-24)

• make average_biological_replicates_dt more restrictive - fewer columns to check for duplicates

gDRutils 2024-10-11 (2024-10-11)

• make duplicates' helpers supporting combo assays as well

gDRutils 2024-10-07 (2024-10-07)

• refactor the logic for dealing with duplicates in assay data

gDRutils 2024-10-03 (2024-10-03)

• fixed issue in average_biological_replicated (fit_type)

gDRutils 2024-09-16 (2024-09-16)

• add functions set_unique_cl_names_dt and set_unique_drug_names_dt

gDRutils 2024-09-04 (2024-09-04)

• remove hack with checkDimnames

gDRutils 2024-08-30 (2024-08-30)

• remove GDS fit_source from gDRviz

gDRutils 2024-08-28 (2024-08-28)

• extend the logic of get_additional_variables to support other sources of fitting metrics

gDRutils 2024-08-14 (2024-08-14)

• extend the logic of average_biological_replicates_dt to calculate standard deviation

gDRutils 2024-08-06 (2024-08-06)

• add functions for setting unique identifiers in the colData and rowData of SE

gDRutils 2024-07-30 (2024-07-30)

• refactor average_biological_replicates_dt and get_additional_variables to support unprettified identifiers

gDRutils 2024-07-17 (2024-07-17)

• update define_matrix_grid_positions

gDRutils 2024-07-12 (2024-07-12)

• move get_combo_col_settings and get_iso_colors to gDRplots package

gDRutils 2024-07-08 (2024-07-08)

• add residual sum of square and p-value to Metrics assay

gDRutils 2024-07-03 (2024-07-03)

• add vignette section about prettifying logic

gDRutils 2024-06-24 (2024-06-24)

• fixed issue in vignette

gDRutils 2024-05-27 (2024-05-27)

• synchronize Bioconductor and GitHub versioning

gDRutils 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

gDRutils 2024-05-17 (2024-05-17)

• simplify logic of supported experiments

gDRutils 2024-05-16 (2024-05-16)

• move define_matrix_grid_positions and round_concentration functions from gDRcore package

gDRutils 2024-05-08 (2024-05-08)

• fix typo

gDRutils 2024-04-30 (2024-04-30)

• move validator functions from gDRcomponents to gDRutils

gDRutils 2024-04-15 (2024-04-15)

• add get_testdata_combo and get_testdata_codilution

gDRutils 2024-03-07 (2024-03-07)

• clean up the package

• simplify keywords

gDRutils 2024-02-28 (2024-02-28)

• add fit_source to header list

gDRutils 2024-02-26 (2024-02-26)

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

gDRutils 2024-02-22 (2024-02-22)

• restore tooltips in table

gDRutils 2024-02-14 (2024-02-14)

• make documentation compatible with pkdgdown

gDRutils 2024-01-30 (2024-01-30)

• rename matrix into combination

gDRutils 2024-01-22 (2024-01-22)

• add new description fields

gDRutils 2023-12-01 (2023-12-01)

• fix bug with refining rowData
• extend the list of headers

gDRutils 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

gDRutils 2023-10-24 (2023-10-24)

• release Bioc 3.18

• prerelease Bioc 3.18

gDRutils 2023-10-18 (2023-10-18)

• adjust NEWS to Bioc format

gDRutils 2023-10-09 (2023-10-09)

• add support for flattening averaged assays

gDRutils 2023-09-22 (2023-09-22)

• fix bug in the case of conc=0 for evaluating efficacy

gDRutils 2023-09-19 (2023-09-19)

• add wide_structure param to convert_mae_assay_to_dt

gDRutils 2023-09-08 (2023-09-08)

• updated experimentalist description in schema

gDRutils 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

gDRutils 2023-08-01 (2023-08-01)

• keep unchanged names in DataFrame

• tidy code

gDRutils 2023-06-27 (2023-06-27)

• add assert for missing rownames

gDRutils 2023-06-22 (2023-06-22)

• replaced RDS with qs

gDRutils 2023-06-20 (2023-06-20)

• fix check in R 4.3

gDRutils 2023-06-12 (2023-06-12)

• switch from merge to [[

• replace order with data.table::setorder
• add support for custom identifiers in merge_SE

gDRutils 2023-06-07 (2023-06-07)

• switch from aggregate to data.table

gDRutils 2023-06-06 (2023-06-06)

• replaced reshape2 functions by functions from data.table

gDRutils 2023-05-22 (2023-05-22)

• format the vignette with BiocStyle

• fix related with data.table
• remove .get_treated_conditions and .get_untreated_conditions

gDRutils 2023-05-18 (2023-05-18)

• add support for merging combination-data assays

gDRutils 2023-05-12 (2023-05-12)

• update after unifying normalization types

• fix lintr

gDRutils 2023-05-09 (2023-05-09)

• removed cotreatment entry from EXPERIMENT_GROUPS

• fix bug in convert_mae_assay_to_dt

gDRutils 2023-05-08 (2023-05-08)

• refactor code with single ampersand in if statements

gDRutils 2023-04-28 (2023-04-28)

• change order of untreated tags

gDRutils 2023-04-24 (2023-04-24)

• changed data.frame to data.table

gDRutils 2023-04-20 (2023-04-20)

• switch to OSI license

• clean-up vignette

gDRutils 2023-04-18 (2023-04-18)

• extend the logic of apply_bumpy_function

gDRutils 2023-04-17 (2023-04-17)

• add R 4.2 as a dependency

gDRutils 2023-04-14 (2023-04-14)

• fix examples

gDRutils 2023-04-13 (2023-04-13)

• make linter happy

gDRutils 2023-04-12 (2023-04-12)

• add license

gDRutils 2023-04-07 (2023-04-07)

• update maintainer

gDRutils 2023-03-28 (2023-03-28)

• downgrade version to make it Bioconductor compatible

gDRutils 2023-03-13 (2023-03-13)

• tidy code

gDRutils 2023-03-09 (2023-03-09)

• better handling of corner cases for the single-agent fitting

gDRutils 2023-03-08 (2023-03-08)

• add support for splitting normalization data types

• restore necessary functions

gDRutils 2023-03-01 (2023-03-01)

• add examples of identifiers

• remove obsolete code

gDRutils 2023-02-22 (2023-02-22)

• tidy code

gDRutils 2023-02-10 (2023-02-10)

• add tests for convert_se_ref_assay_to_dt

gDRutils 2023-01-10 (2023-01-10)

• add helpers for colData/rowData refinement

gDRutils 2022-12-22 (2022-12-22)

• fix warnings in unit tests

gDRutils 2022-12-20 (2022-12-20)

• R CMD check returns 0 errors ✓ | 0 warnings ✓ | 0 notes ✓

gDRutils 2022-12-15 (2022-12-15)

• default apply_bumpy_function parallelize to TRUE

gDRutils 2022-12-08 (2022-12-08)

• add apply_bumpy_function support

gDRutils 2022-12-07 (2022-12-07)

• add co-dilution to single-agent group

gDRutils 2022-11-30 (2022-11-30)

• bugfix in validate_SE

gDRutils 2022-10-18 (2022-10-18)

• add update_env_idfs_from_mae function

gDRutils 2022-10-04 (2022-10-04)

• add helper for dealing with idfs' synonyms

gDRutils 2022-09-21 (2022-09-21)

• promote or demote fields in a BumpyMatrix object and perform summarization on assays.

gDRutils 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

gDRutils 2022-07-25 (2022-07-25)

• move json validation/conversion logic from gDRelastic

gDRutils 2022-07-11 (2022-07-11)

• standardize MAE using default gDR identifiers

gDRutils 2022-06-29 (2022-06-29)

• remove adding integer identifiers at the end of colnames/rownames

gDRutils 2022-06-02 (2022-06-02)

• release 1.3.0

gDRutils 2022-05-27 (2022-05-27)

• correct recognition of empty SE

gDRutils 2022-05-25 (2022-05-25)

• remove redundant validation of rownames in SE

gDRutils 2022-05-03 (2022-05-03)

• update prettify function
• fix hardcoded identifiers in validated_SE

gDRutils 2022-04-29 (2022-04-29)

• avoid using grep for getting cotreatment identifiers

gDRutils 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

gDRutils 2022-04-13 (2022-04-13)

• set r2 value to NA for invalid and 0 for constant fits

gDRutils 2022-04-08 (2022-04-08)

• added identifier descriptions

• fix wrong order of elements in rownames in SE

gDRutils 2022-04-07 (2022-04-07)

• add cap_ic50 function

gDRutils 2022-03-31 (2022-03-31)

• extend possible Barcode identifiers

gDRutils 2022-03-30 (2022-03-30)

• fix hardcoded identifiers in validate SE

gDRutils 2022-03-28 (2022-03-28)

• add a space between two-word cotreatment identifiers

gDRutils 2022-03-24 (2022-03-24)

• remove all R CMD check warnings

gDRutils 2022-03-22 (2022-03-22)

• change prettify functions to not substitute metadata

gDRutils 2022-03-21 (2022-03-21)

• add helper function for MAE/experiments

gDRutils 2022-03-19 (2022-03-19)

• move constant fit warning

gDRutils 2022-03-18 (2022-03-18)

• add .calculate_complement

gDRutils 2022-03-16 (2022-03-16)

• move duplication warning

gDRutils 2022-03-14 (2022-03-14)

• add support for identifier validation

gDRutils 2022-03-03 (2022-03-03)

• add getter and setter for experiment_raw_data

gDRutils 2022-02-16 (2022-02-16)

• refactor identifier drugname to drug_name

gDRutils 2022-02-10 (2022-02-10)

• add MAEpply function

gDRutils 2022-02-01 (2022-02-01)

• update documentation

gDRutils 2022-01-31 (2022-01-31)

• support SE- init for different BioC versions

gDRutils 2022-01-25 (2022-01-25)

• standardize/improve CI

• switch unit tests from SE to MAE from gDRtestData

gDRutils 2022-01-07 (2022-01-07)

• update assert in validate_MAE

• update SE-related functions of gDRutils to support MAE

gDRutils 2021-12-21 (2021-12-21)

• move combo-related functions from gDRviz
• add unit tests for combo-related functions

gDRutils 2021-11-04 (2021-11-04)

• do not create a nested list of identifiers during merging SE

gDRutils 2021-11-01 (2021-11-01)

• fix issued with new SummarizedExperiment

gDRutils 2021-10-22 (2021-10-22)

• refactor: generalize prediction help functions for fits

gDRutils 2021-09-27 (2021-09-27)

• update validate_SE as per combos

gDRutils 2021-09-22 (2021-09-22)

• feat: use 'GRvalue' and 'RelativeViability' as normalization_types in 'fit_curves'

gDRutils 2021-09-15 (2021-09-15)

• fix bug with getting_SE_identifiers for untreated_tag

gDRutils 2021-09-13 (2021-09-13)

• fix obsolete arguments in reset_env_identifiers

gDRutils 2021-09-07 (2021-09-07)

• fix bug with getting identifiers for untreated_tag

gDRutils 2021-08-26 (2021-08-26)

• move NA logic for elements of BumpyMatrix with no data to fit_curve

gDRutils 2021-08-25 (2021-08-25)

• remove additional ordering line in df_to_bm_assay.R

gDRutils 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-

gDRutils 2021-08-13 (2021-08-13)

• fix bug with wrong order of rows and cols in df_to_bm_assay

gDRutils 2021-07-06 (2021-07-06)

• remove hard version equality for pkg deps

gDRutils 2021-06-29 (2021-06-29)

• add barcode as identifiers and store identifiers within split_SE_components

gDRutils 2021-06-25 (2021-06-25)

• update the logic for CI/CD - repos fetching is now handled with technical user

gDRutils 2021-06-21 (2021-06-21)

• refactor logisticFit with error handling

gDRutils 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

gDRutils 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

gDRutils 2021-05-24 (2021-05-24)

• refactor validate_SE function

gDRutils 2021-05-18 (2021-05-18)

• add merge_SE function

• fix typo in SE validator function

• add SE validator function

gDRutils 2021-05-13 (2021-05-13)

• refactor prettify_flat_metrics function

gDRutils 2021-04-30 (2021-04-30)

• remove Metrics_rownames during flattening data.frame/data.table

gDRutils 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

gDRutils 2021-04-27 (2021-04-27)

• add support for flattening data.tables

gDRutils 2021-04-21 (2021-04-21)

• switch from processing_metadata to .internal

gDRutils 2021-04-20 (2021-04-20)

• add support for getting and setting processing info metadata

gDRutils 2021-04-19 (2021-04-19)

• sort BumpyMatrix created from dt

gDRutils 2021-04-14 (2021-04-14)

• revert metric arguments in 'convert_se_assay_to_dt'

gDRutils 2021-04-09 (2021-04-09)

• add support for getting and setting fit parameter metadata

gDRutils 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

gDRutils 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

gDRutils 2021-03-23 (2021-03-23)

• remove positional naming dependence on assay_to_dt for - merge_metrics = TRUE argument

gDRutils 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

gDRutils 2021-03-09 (2021-03-09)

• update .estimate_xc50 and add tests

gDRutils 2021-03-04 (2021-03-04)

• fix bug with wrong class for S3 methods in convert_assay_data_to_dt
• update the documentation

gDRutils 2021-03-02 (2021-03-02)

• fix bug with missing class in assert for matrix

gDRutils 2021-02-10 (2021-02-10)

• modify fit_curves to take in flexible curve_type- s
• clean-up assay_to_dt

gDRutils 2021-02-04 (2021-02-04)

• added linter

gDRutils 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

gDRutils 2021-01-26 (2021-01-26)

• allow for DFrame as input

• 's/BumpyMatrix::splitToBumpyMatrix/BumpyMatrix::splitAsBumpyMatrix/'

gDRutils 2021-01-20 (2021-01-20)

• refactor RVGRfits and rename to fit_curves
• make logisticFit function independent of curve_type

gDRutils 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

gDRutils 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

gDRutils 2020-10-12 (2020-10-12)

• add CI

gDRutils 2020-10-09 (2020-10-09)

• fix assay_to_df

• update namespaces

gDRutils 2020-10-05 (2020-10-05)

• minor refactor

gDRutils 2020-09-14 (2020-09-14)

• add small fixes for assays with empty DataFrame

gDRutils 2020-09-02 (2020-09-02)

• update logic as per new db model

gDRutils 2020-08-07 (2020-08-07)

• update variable names as per new db model

gDRutils 2020-07-02 (2020-07-02)

• import pipes from magrittr

gDRutils 2020-06-10 (2020-06-10)

• including the masked field to be able to remove the masked data from averages