NEWS

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CytoPipeline 1.5

CytoPipeline 1.5.2

• updated unit test to account for flowAI version change
• now suggesting CytoPipelineGUI package

CytoPipeline 1.5.1

• updated processing step argument matching using phenoData

CytoPipeline 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

CytoPipeline 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