- fix melt error after changed
intersect
behaviour
- fix melt in annotation function to fix Bioc error
- synchronize Bioconductor and GitHub versioning
- hot fix for annotation colnames of cell lines
- split and refactor annotation functions
- add support for reprocessing data with old data model
- handle properly additional perturbations to get rid of creating additional columns that can't be hangle properly by the app
- identify additional perturbations hidden in the secondary drug
- utilize
calc_sd
function
- fix issue with wrong mapping of Day0 data
- fix issue with mapping overrides untreated controls
- fix issue with non-avearaged concentration data
- fix issue with providing empty nested_confounder
- allow using custom functions for calculating HSA and Bliss scores for combination data
- refactor logic for calculating standard deviation for single values
- update unit tests
- switch to
get_supported_experiments
- synchronize Bioconductor and GitHub versioning
- move
define_matrix_grid_positions
andround_concentration
functions togDRutils
package
- add functions for retrieving annotation data from input dt
- fix typo
- add vignette with documentation for data annotation
- add support for external annotation specified in the env var
- fix bug with converting mae into raw_data
- remove unstable tests
- cleanup package
- update function description
- improve pkgdown site
- improved references
- valid NEWS.md
- fix issue with retrieving unique records from mix of control and treated samples
- make documentation compatible with pkdgdown
- rename 'matches' to 'grr_matches'
- fix unit tests for GRAN
- simplify logic of assays for combination data
- rename
matrix
intocombination
- add support for internal source of annotation
- fix bug with converting standardize MAE into raw data
- add vignette for a data model
- update wrappers for co-dilution data
- add new description fields
- improve logic for normalization and identification of single-agent and matrix data with Drug3
- fix issue with wrong assignment of
untreated
records
- sync master with devel branch
- add support for unifying duplicates in combo matrix data
- add "Treatment" as template identifier
- release Bioc 3.18
- prerelease Bioc 3.18
- adjust NEWS to Bioc format
- bump version of gDRtestData
- fix bug with merging controls in triple combo with additional perturbations
- add support for adding custom annotations inside input files
- improve the performance
- fix bug with subsetting wrong combo matrix value
- extend the logic for matching missing controls
- set Drug3 as an official tertiary drug in the experiment
- fill NA by average values when there is no match with plate
- fill NA during aggregation of ref and trt data with mean
- fix issue with missing subsetting Day0 data
- update logic for supporting manifest and template files sharing the same column
- update annotation column names for cell line annotation as per changes in the gDRutils
- extend logic for supporting cols with dash, e.g. additional perturbations with "-"
- update the logic for handling warnings in the pipeline
- fix issue with wrong merging of data.tables without nested confounders
- add information about source type for cases without metric data
- refactor the logic for splitting raw data from metadata - get rid of iterative approach
- update logic for parallel computing
- optimize unit tests
- remove backward compatibility for old data model
- fix bug with missing rownames in normalized assay
- update logic for merging data.table objects
- replace
order
withdata.table::setorder
- switch from
merge
to[[
fordata.table
objects
- switch from
aggregate
todata.table
- switch from
zoo::rollmean
todata.table::frollmean
- replace reshape2 functions by functions from data.table
- fix managing of mixed types of raw data
- fix bug with subsetting data for calculating isobologram
- format the vignette with BiocStyle
- fix related with data.table
- rename
excess
tox
to unify colnames in assay data
- refactor normalization_types in combo-specific assays
- utilize
gDRutils::apply_bumpy_function
in fit_SE
- fix bug with swapping untreated/vehicle values
- fix bug with data.table
- utilize
gDRutils::apply_bumpy_function
in average_SE
- switch to OSI license
- fix bug with replacing vehicle to untreated values
- moved wrapper fuctions from gDRtestData
- update dependencies
- add fix for bioc-devel - correct sorting in merge test
- fix namespacing issue in examples
- add R 4.2 as dependency
- fix examples for normalize_SE
- add logic for retrieving raw data from assay data
- update maintainer
- bugfix for the logic in 'cleanup_metadata'
- make the package Bioc-compatible
- improve performance of 'map_df' with refactored logic for exact matches
- refactor pipeline
- address co-treatment fit by using the matrix data type instead
- add support for splitting normalization types
- improve logic in functions used to generate isobolograms' data
- remove obsolete code
- add support for partial pipeline runs
- update path to annotation data
- clean-up code
- clean-up code
- refactor mapping function to properly handle drug3
- replace parallelize function with gDRutils::loop
- add assert for vehicle values in input data in
runDrugResponseProcessingPipeline
- fix error-handling if conditions in average_SE
- fix invalid encapsulation in tests
- add missing namespacing
- add support for setting number of cores for
BiocParallel
based on the env variable
- remove global parameters for
BiocParallel
- change the logic for using cores in
BiocParallel
- update the logic for parallel computing
- update the logic for default nested_confounders in
create_SE
function
- refactor create_SE to support reverse single-agent data
- release 1.3.0
- add missing namespace for get_env_identifiers
- replace
NA
by 0 in Concentration loaded in manifest file
- switch from
data.table
todata.frame
in add_annotation* functions
- update function for adding unknown cell line annotations
- update logic for using nested confounders
- remove
grr
from dependencies
- get rid of gDRwrapper
- add support for additional barcode identifiers
- fix documentation in calculate_matrix_metric
- switch from
catchr
topurrr
- fix mapping reference values of inverted treatments
- remove duplication of single-agent data
- wrap SE into MAE on the level of runDrugResponseProcessingPipeline
- change identifier
drugname
todrug_name
- switch from
gDRinternal
togDRinternalData
for internal annotations
- issue with subsetting by list in R 4.2.0
- unlist output of intersect as per R 4.2.0
- align version criteria between
dependencies.yaml
andDESCRIPTION
package versions
- standardize/improve CI
- switch from
cores
variable todetect_cores-
function
- fix wrong type of
NUM_CORES
env variable
- speed-up functions for mapping treated and untreated cases
- fix linter issues
- use parallel computing as an alternative for
for
loops
- update annotation script as per new csv annotation files
- detect co-trt data and treat them as single-agent
- set excess = NA for single-agent
- solve rounding issues
- add new bliss metric
- refactor isobolograms
- move p_trt_keys to the proper place
- add support for masked data in fit_SE.combinations.R
- address issues in creating the SE for combo matrix experiments
- refactor the logic for calculation Loewe when there is no
Concentration == 0
- refactor the logic for combo data
- updated normalization_types in 'calculate_combo_matrix' and 'fit_SE'
- calculate_GR_value by removing cl_name param
- fix but with missing
nested_identifiers
variables for creating DataFrame for masked values
- refactor reading annotations and add default parameters
- fix bug for nested_confounders not present in ref_df
- add support for nested_identifiers and nested_confounders
- remove obsolete dependencies from DESCRIPTION:Imports
- function for testing synthetic data
- move functions for importing template files to gDRimport package
- add linter
- remove obsolete functions from test.utils.R
- move importing functions to gDRimport package
- add unit tests for synthetic data
- remove deprecated functions and unit tests
- update namespace for 'metadata- '
- change package name - gDR => gDRcore
- export/update docs for 'standardize_record_values'
- release 1.0.0
- remove all the gDRinternal-related files
- fix wrong argument name in
fit_curves
- ensure that dts in
assay- se,"Averaged"
are NULL when there are not treatments
- add processing info metadata to SE
- improve handling of nested_keys and override_controls
- get rid of sorting index columns in getMetaData
- move SE metadata getters and setters to gDRutils
- fix a bug in map_df function
- refactor processing functions in create_SE2, normalize_SE2, average_SE2, and fit_SE2 and friends
- add drug_moa_2 to merged df
- fix a bug with adding annotation to codrugs
- add script for benchmarking [normalize/average/metrics]-SE functions
- fix unit tests
- include discard keys info in getMetaData for rowData
- utilize refactored and renamed fitting function RVGRfit to fit_curves
- export some functions for use in gDRutils
- move df_to_assay and df_to_bm_assay to gDRutils
- updated rowData and colData in SE with additional columns
- update positional header calls to explicit identifier calls
- minor changes to comply with gDRstyle
- minor changes to use identifiers over hard coded DrugName requirements
- update scripts related to annotation of drugs and cell lines
- anonymize test data
- switch from GeneDataScreenR to gDRinternal from QCS to gDR functions
- 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
- minor clean-up
- remove dplyr
- use the latest version of gDRutils
- error messages
- refactor analyze_data.R with taking account codilution combo
- bug with reading raw data
- clean-up repository from duplicated functions
- switch to R 4.0
- bugs in function for metrics calculation as per QCS dataset
- QCS data
- scripts for processing and pushing QCS data on Rosalind
- updated README.md
- bug in update_experiment_metadata
- logic as per new db model
- RDS files for the other GDS data - GDS5, GDS6, GDS7
- 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
- fixed issue in update_experiment_metadata.R
- unit test for update_experiment_metadata.R
- function for updating metadata in SE
- dependencies: kcloak, gDRwrapper
- dependencies