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some changes in the filter definition that were needed for flowClust integration
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making sure the data is copied when generating a workflow
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adding a coersion method to manyFilterResult
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Cleaned up some of my comments.
Perry's updates to the introduction and conclusions.
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Bumped version no
Updated biexponential transform so that it now calculates
the solution of a generic biexponential function
S(x,a,b,c,d,f) = ae^(bx) -ce^(-dx) +f instead of the logicle function
it was calculating earlier.
Updated Logicle transformation: The implementation of the logicle
transform
was found to be different from that described by Parks et al. A new C
function
was implemented for the logicle transformation reflecting the method
described
in the paper. Additionally, the parameter argument f passed to the
logicle
function was missing a multiplying factor a.
fixing the subsetting of views
We want to be able to add numerics or characters to a workflow
adding support for subsetting operations in workFlows
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add elements in the papaer, especially in the Results and Discussion section
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added vectorized version of figure 1
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update to close connection on exit
added a isFCSfile function
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making sure all parameters in a flowSet are the same
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added flowQ figure to paper
some updates to the paper
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Fixed man page link issue.
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some more coercion methods
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We are able to read files without PnE keyword now. The default of '0,0' is used and a warning is issued
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added a more programatic interface to create transformMaps
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changed eval methods for polytope and ellipsoid gates
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adding functions to write flowFrames and flowSets to FCS files
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Fixed issue with the wrong min range when reading in a fcs file , bumped version no
making sure the range parameter is ignored for clipping after the data has been transformed
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more on the outline
more cleaning up of name space
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fixed hyperlog transforms, compensation and added EH transforms
dealing with conflicts between Florians and Nishants versions
started to clean up the classes
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fixed bug in coercion to flowFrame for empty frames
added import for plot generic
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more updates to the documenation an a number of little buf fixes
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Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
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fixing some issues with manyFilterResults
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another for subsetting of empty flowFrames
fixing bug when subsetting empty flowFrames
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bumping version
fixing some minor issues with keywords
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changed the link fin filter-methods from itself to Subset
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fixed bug in splitting of flowSets by factors
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fixed a number of bugs in data import and basic plotting functions
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changes suggested by Ryan and Josef
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some changes of the paper and addition of work flows
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we are a bit more relaxed about this 10 bit bug in BC FCS files now. When we see the CPX keyword we warn that we fixed the file, if it's not there we still proceed (with 16 bit) but give a more urgent warning
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more verbose error messages when getting out of index on a filter
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more updates to the documenation an a number of little buf fixes
many little fixes of the documentation
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bumping version
'readFlowSet' was overly verbose
allowing to use transformList objects in transform calls
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moved all plotting stuff to flowViz, flowCore now issues a message to attach flowViz for all plotting
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updated docs for transformations
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fixed some minor bugs in the ncdf stuff and bumped version number
introducing netcdf storage for flowFrames
undo mechanism for workFlows and error handling
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fixed warnings for missing documenation during R CMD check
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initialisation method for flowFrame
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update to documentation and addition of methods
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