NEWS

---

CytoPipeline 1.11

CytoPipeline 1.11.1

• Bug correction for scale transfo pipelines with sample specific data: implemented a work-around in readSampleFiles(): forced flowSet sample names to full file paths as this was not done automatically by flowCore::read.flowSet().
• estimateScaleTransforms() now has ... in parameter list, allowing to pass additional parameters to flowCore::estimateLogicle().

CytoPipeline 1.9

CytoPipeline 1.9.4

• improved aggregateAndSample() added a setup parameter, such that when it is equal to "forceNEvent", the nb of events selected per flow frame is not always balanced, to always obtain nTotalEvents (except when the total nb of available events, taking all flowFrames, is less than nTotalEvents).

CytoPipeline 1.9.3

• added sampleDisplayNames()

CytoPipeline 1.9.2

• sample files can now have duplicate base names (provided full paths are different)
• pData<- is now more liberal.

1. It can accept new pData containing more rows than existing sample names (the corresponding subset of pData is taken).
2. It can accept pData with row names pointing to either sample file full paths or base file names
3. It can accept pData with no row names provided the number of rows correspond to the number of sample files. Row names are then set by default to sample file base names (if unique), or sample file full paths.

CytoPipeline 1.9.1

• upgraded to GHA cache v4

CytoPipeline 1.7

(no devel)

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