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Releases: kuwisdelu/Cardinal

Cardinal 3.6.4

14 Jul 00:40
@kuwisdelu kuwisdelu
v3.6.4
b6131f2
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Cardinal 3.6.4 Latest
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CHANGES IN VERSION 3.6.4 [2024-7-13]

BUG FIXES

o Bug fixes for 'plot()' on spectra with queued processing
Assets 2
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Cardinal 3.6.3

26 Jun 22:36
@kuwisdelu kuwisdelu
v3.6.3
cf3af2a
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Cardinal 3.6.3

CHANGES IN VERSION 3.6.3 [2024-6-26]

BUG FIXES

o Bug fixes for 'meansTest()' when random effects are specified
Assets 2
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Cardinal 3.6.2

13 Jun 16:10
@kuwisdelu kuwisdelu
v3.6.2
1c6249e
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Cardinal 3.6.2

CHANGES IN VERSION 3.6.2 [2024-6-10]

BUG FIXES

o Version bump for 'matter' 2.6.2 bugfixes

CHANGES IN VERSION 3.6.1 [2024-5-17]

SIGNIFICANT USER-VISIBLE CHANGES

o Add 'mass.range' and tolerance' arguments to 'bin()'

BUG FIXES

o Fix 'readImzML' error if imzML fails conversion to 'ImzMeta'

CHANGES IN VERSION 3.5.6 [2024-4-26]

SIGNIFICANT USER-VISIBLE CHANGES

o Add optional 'run' argument to 'slice()'
o Add optional 'plotly' support for all plotting methods

CHANGES IN VERSION 3.5.5 [2024-4-25]

BUG FIXES

o Fix bug in 'selectROI()' region plot updates

CHANGES IN VERSION 3.5.4 [2024-4-24]

NEW FEATURES

o Re-add support for 3D coordinates and 'image3D()'

SIGNIFICANT USER-VISIBLE CHANGES

o Export 'vizi_style()' and 'vizi_engine()' functions
o Add 'check' argument to 'readMSIData()' for uuid+checksum

BUG FIXES

o Fix bug in plotting PLS/OPLS coefficients
o Fix removing position columns with 'coord()<-'

CHANGES IN VERSION 3.5.3 [2024-4-13]

NEW FEATURES

o Add support for multiple instance learning for 'PLS()'
    and 'spatialShrunkenCentroids()' with 'bags' argument
o Add 'estimateReferenceMz()' for more easily estimating
    profile m/z-values from 'MSImagingArrays'

BUG FIXES

o Make sure 'bin()' still respects 'resolution' when 'ref' is
    specified (in which case the range is taken from 'ref')
o Fix 'crossValidate()' for multiple instance learning

CHANGES IN VERSION 3.5.2 [2024-4-13]

BUG FIXES

o Fix passing 'tolerance' in 'peakProcess()' when not needed
o Fix bugs in 'selectROI()' not updating the plot
o Fix bugs in 'selectROI()' selecting wrong pixels
o Make sure 'peakAlign()' produces similar results when
    re-aligning peaks with the same tolerance

CHANGES IN VERSION 3.5.1 [2024-4-7]

NEW FEATURES

o Ground-up rewrite to take advantage of matter v2.5 features
o New class 'SpectraArrays' for arrays of spectra
o New class 'SpectralImagingData' for spectral imaging data
o New class 'SpectralImagingArrays' for raw spectra
o New class 'SpectralImagingExperiment' for centroided spectra
o New class 'MSImagingArrays' for raw mass spectra
o Updated class 'MSImagingExperiment'
o Updated class 'XDataFrame'
o Updated classes 'PositionDataFrame' and 'MassDataFrame'
o New apply method 'spectrapply()'
o New processing method 'recalibrate()'
o New processing method 'bin()'
o New processing method 'peakProcess()'
o New classes 'SpatialResults' and 'ResultsList'
o Updated spatial methods 'findNeighbors()' and 'spatialWeights()'
o Updated spatial methods 'colocalized()'
o Updated projection methods 'PCA()' and 'spatialFastmap()'
o New projection method 'NMF()'
o Updated stats methods 'PLS()' and 'OPLS()'
o Updated stats method 'spatialKMeans()'
o Updated stats method 'spatialShrunkenCentroids()'
o Updated stats method 'spatialDGMM()'
o Improved visualization methods 'plot()' and 'image()'

SIGNIFICANT USER-VISIBLE CHANGES

o Deprecated 'smoothSignal()' -- use 'smooth()'
o Deprecated 'mzBin()' -- use 'bin()'
o Deprecated 'mzAlign()' -- use 'recalibrate()'
o Deprecated 'mzFilter()' -- use 'subsetFeatures()'
o Deprecated 'peakFilter()' -- use 'subsetFeatures()'
o Deprecated 'aggregate()' -- use 'summarizeFeatures()'
o Deprecated 'featureApply()' -- use 'summarizeFeatures()'
o Deprecated 'pixelApply()' -- use 'summarizePixels()'
Assets 2
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