Bump of major version for official release and publication
Changed order of events in the prep_fcd function. This makes the process faster (especially in smaller machines) and reduces the usage of memory.
Added function subset_fcd_byparam. This function allows to randomly subset a condor object proportionally across a selected parameter. For example is not possible to randomly subset n cells from each samples.
Included more professionalization in the read_fcd function. This allows the user to customize few aspects of the condor object
Included cyCONDOR version in the condor object under the extras slot. This enables the user to trace the version used for the analysis.
cyCONDOR 0.1.6
Reorganization of existing visualization functions including harmonization of function names and function arguments, utilization of condor object as main input object and addition of more extensive documentation and error messages.
Added getTable() function to generate tables of cell population counts and frequencies, as well as mean or median marker expression for all cell population - sample - marker combinations.
boxplot_and_stats() function was replaces by plot_frequency_boxplot() function for visualization and several functions to conduct statistical tests on population frequencies.
Added prepInputDiffcyt() function to transform the condor object into an SummarizedExperiment object compatible with the diffcyt package for differential testing.
Renaming of arguments in runPseudotime() function to harmonize within the package
Renaming of arguments in metaclustering() function to harmonize within the package
Updated documentation
Renaming of arguments in multiple function to harmonize within the package
Setting a default seed in multiple functions
Added functions to use the CytoNorm algorithm for batch normalization
Bug fixes in prep_flw() when merging annotation and removing parameters, saving of import parameters in extras slot of fcd
Added new parameters in runFlowSOM() to determine size of FlowSOM grid