Changes in version 1.3 CytoPipeline 1.3.6 - execute() now stores the nb of events retained at each pre-processing step, to speed-up collectNbOfRetainedEvents() CytoPipeline 1.3.5 - added CITATION file CytoPipeline 1.3.4 - in execute(), when cache does already exist, make it clean before executing the pipeline steps (= preventing inconsistent cache upon crash/forced interruption) CytoPipeline 1.3.3 - added collectNbOfRetainedEvents() function CytoPipeline 1.3.2 - systematically override pData in cache upon execute() to allow running consistently running several times for increasing number of samples - sampleFiles<- and pData<-: make sure that order of sample files follow the one of pData rownames if pData exists. - added 'verbose' argument in estimateScaleTransforms() CytoPipeline 1.3.1 - refactored documentation files Changes in version 1.1 CytoPipeline 1.1.5 - areSignalCols(), are FluoCols() can now accept a flowSet as input, on top of a flowFrame - applyScaleTransforms() processing step has been improved (can take flowSet as input, checks channel concordance between transList and data object) CytoPipeline 1.1.4 - updated fcs files, that are at the source of OMIP021Samples dataset CytoPipeline 1.1.3 - in subSample(), renamed parameter 'nSamples' into 'nEvents', and added possibility for passing unused parameters, in order to support the use of the function as a processing step. Also amended the function as to keep the original order of the events (keep chronology). Finally, adds a 'keepOriginalCellIDs' parameter (default=TRUE). - simplified the arguments of execute() related to the storage of the results after last pre-processing step. CytoPipeline 1.1.2 - storage of phenoData into cache upon execution of CytoPipeline object (and back into CytoPipeline object when re-built from cache) - changed the default behaviour of estimateScaleTransforms() so that the default method for scatter channels is now "none" instead of "linearQuantile" - changed default behaviour of ggplotEvents() and ggplotFilterEvents(), when logicle scale is used but no logicle parameters provided, these are now estimated using flowCore::estimateLogicle(), instead of explicit default values CytoPipeline 1.1.1 - tiny modifications to support upgrade to Bioc 3.18 CytoPipeline 0.99 CytoPipeline 0.99.6 - corrected the OMIP021Samples fcs data in order to keep the original file name - bug correction: error message on execution with no sample file - added phenoData slot in CytoPipeline object - updated readSamples() to allow passing a pData parameters - updated compensateFromMatrix() to allow passing a mapping based on a pData variable - updated readSamples() to allow selecting a random number of samples and removed selectSamples() - vignette with demo and links to videos CytoPipeline 0.99.5 - reactivated unit tests for ggplot2 objects - added man page for CytoPipeline package - a few modifs in the vignette related to Bioc review process - replaced withr::local_tempdir() by base::tempdir() - removed extraneous whitespaces in CytoPipeline show() method - removed LazyData: true in DESCRIPTION file - replaced paste0(path, "/", filename) by file.path(path, filename) - updated License field in DESCRIPTION file CytoPipeline 0.99.4 - improved CytoPipeline constructors (experimentName and sampleFiles are now parameters of all constructor version) - centralized the production of standard outputs during pipeline execution, set all tuning parameters in execute() instead of slots in CytoPipeline object. CytoPipeline 0.99.3 - some minor changes for BiocCheck() CytoPipeline 0.99.2 - removed dependencies to a number of packages, moved corresponding implementations of CytoProcessingSteps (wrappers) into CytoPipelineUtils package CytoPipeline 0.99.1 - Maintenance due to Bioc version change (3.17) - removed use of openCyto::gate_tail() (disappeared w/o deprecation), replaced by flowDensity::deGate() - implemented export of pre-processed file (writeFlowFrame as a CytoProcessingStep implementation) - extended readSampleFiles : mapping between channels and markers - selectRandomSamples (new CytoProcessing step implementation) CytoPipeline 0.99.0 - Prior to Bioconductor submission