Version 1.1.7
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* Small changes in the documentation (in particular, explaining in the
  README's FAQ section when to use the *mRNAProportions* or *cellFractions*).
* Removed the warning message about unknown *mRNA_cell* values that was written
  nearly in all runs (writing the caution message about this directly in the FAQ
  section).
* Corrected a bug when there were duplicated *empty* gene names (i.e., genes
  named simply as "").

Version 1.1.6
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* Changed person of contact for commercial licenses to Nadette Bulgin.

Version 1.1.5
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* Renamed EPIC's vignette to call it through "vignette('EPIC')"

Version 1.1.4
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* EPIC now handle cases of duplicate gene names in the input bulk or reference
  profiles.
* Small updates to the documentation of EPIC package.

Version 1.1.3
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* Various small updates to the documentation of EPIC package.

Version 1.1.2
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* Updates in the documentation to include the reference to EPIC paper that has
  now been published in eLife.

Version 1.1.1
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* Small updates in README and vignette to add contact information for
  commercial licenses.

Version 1.1.0
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* Change version number to 1.1.0, corresponding to what was used for EPIC
  paper.

Version 1.0.6
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* Updated EPIC to use the latest reference profiles and updated some default
  values and tests for the package.
* Updated the help files accordingly, explaining also the additional advanced
  options available for EPIC.

Version 1.0.5
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* Updated EPIC to remove genes from bulk that have only NA values.

Version 1.0.4
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* Changed the name "scaleRefProf" to "scaleExprs" and made this boolean makes
  that either both bulk data and reference profile are rescaled internally (by
  default), or that none of them is rescaled.
* Added the option "constrainedSum" (default is TRUE). When this is FALSE, we
  release the constrain that the sum of cells with known reference profiles
  must be smaller than 1. Also if withOtherCells is FALSE and constrainedSum is
  FALSE, we don't use the constraint during the optimization that the sum of all
  the cells must also be equal to 1 (note we still rescale afterwards the
  proportions to have a sum equal to 1 but it isn't done during the
  optimization).

Version 1.0.3
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* Little correction in the code to make we can really do the fits without any
  refProfiles.var (to give same weight to each gene in the optimization).
* Addition of the input "withOtherCells" (default to TRUE): when FALSE, we
  assume the bulk is only composed of the cells with known reference profile
  and force thus in the optimization a sum of these cells' mRNA proportions
  to be equal to 1.

Version 1.0.2
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* Added another way to compute the minimum in the optimization, based on the
  ranges from each gene given in the refProfiles.var instead of using simple
  weights based on these.
* Added the option scaleRefProf in EPIC (default to TRUE) to re-scale or not
  the reference gene expression profile based on the gene in common with the
  bulk sample. We can set it to FALSE if we rescale beforehand the ref profile
  based on the mRNA / cell value for example.

Version 1.0.1
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* Removed the warnings from spearman correlation computations indicating that
  the p-value isn't exact in the presence of ties.
* Added mRNA_cell values for T cell subtypes.
* Added reference profiles including CD4 and CD8 T cells for circulating
  immune cells and including also CAFs and endothelial cells for tumor
  infilatring cells.


Version 1.0.0
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* Public release of EPIC package.
