Changelog

Source: NEWS.md

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