CHANGES IN VERSION 1.2.1
------------------------

# Universalizing the versions across GitHub and bioconductor, we are now at 1.2 for bioconductor
# and v1.2.1 for the master. Dev branch will be updated to reflect this change to v1.2.2. Apologies #for the confusion.

* Updated coding practices based on devtools and bioccheck
* Deprecated VizVgene() support - erroring during build and new version in dev branch to visualize any gene
* fixed lengthDF handling of single chains with multi chains stored - ;
* Changed grabMeta to include assessment of colnames
* number of changes to the parseTCR/BCR functions to limit assumptions


CHANGES IN VERSION 1.1.4
------------------------

* replaced hammingCompare with lvCompare to enable superior clonotype calling in combineBCR function.
* added proportion to combineExpression() function so users no longer need to know absolute frequencies when combining the contiguous information. 
* added clusterTCR() and clonalOverlay() functions.
* added downsampling to the diversity calculations
* replaced hammingCompare with lvCompare to enable superior clonotype calling in combineBCR function.
* added proportion to combineExpression() function so users no longer need to know absolute frequencies when combining the contiguous information. 
* added clusterTCR() and clonalOverlay() functions.
* added downsampling to the diversity calculations
* Clonal Overlap Coefficient issue fixed, was comparing unique barcodes and not clonotypes
* Added function checkBlanks to remove list elements without clonotypes, this prevents errors for visualizations
* Re-added Startrac metrics by stripping down the package and adding it piecemeal
* Heavily modified dependencies to reduce total number 


CHANGES IN VERSION 1.0.0
------------------------

* removed dependencies ggfittext and ggdendrogram
* clonesizeDistribution now returns a plot() function


CHANGES IN VERSION 0.99.18
------------------------

* Updated author information in the vignette


CHANGES IN VERSION 0.99.17
------------------------

* Updated NEWS formatting
* Edited DESCRIPTION to SingleCellExperiment R package
* Updated information in the vignette


CHANGES IN VERSION 0.99.16
------------------------

* Added getCirclize() 


CHANGES IN VERSION 0.99.15
------------------------

* Modified numerator for index function


CHANGES IN VERSION 0.99.14
------------------------

* Removed bracket from indexing function

CHANGES IN VERSION 0.99.13
------------------------

* Added exportTable to remaining viz functions
* Modified morisita index to correct error

CHANGES IN VERSION 0.99.12
------------------------

* Reducing the size of the screp_example to fulfill < 5 mB requirement. Randomly samples 100 cells and removed RNA counts from Seurat object

CHANGES IN VERSION 0.99.11
------------------------

* Updated compareClonotype to allow for clonotype comparisons


CHANGES IN VERSION 0.99.10
------------------------

* Bioconductor did not detect the version update.

CHANGES IN VERSION 0.99.9
------------------------

* Bioconductor had no love - changed the Seurat package to imports instead of required, see if that will address the compiling issue that results in a killed: 9 error. 

CHANGES IN VERSION 0.99.8
------------------------

* Passed checks on system, let's see how much bioconductor hates it

CHANGES IN VERSION 0.99.7
------------------------

* But really this time, changed the colData import

CHANGES IN VERSION 0.99.6
------------------------

* Changed colData import

CHANGES IN VERSION 0.99.5
------------------------

* Added screp_example data to package
* Added visVgene function for visualizing the distribution of V genes in TCR
* Added support for monocle to combineExpression function
* Updated documentation for combineTCR() and combineBCR()
* Updated documentation to utilize SingleCellExperiment formats
* Updated Vignette to utilize SingleCellExperiment formats
* Added Author information to vignette
* Add intro and conclusion to vignette
* Removed html knitted vignette
* Removed descriptive code snippets

CHANGES IN VERSION 0.99.4
------------------------

* Modified expression2List() to allow for variables across meta data

CHANGES IN VERSION 0.99.1
------------------------

* Changed R (>= 3.6) to R (>= 4.0)


CHANGES IN VERSION 0.99.0
------------------------

* Changed DESCRIPTION version to 0.99.0
* Removed file seurat_example.rda, accidentally committed
* Deleted git attributes
* reduced Seurat object size for alluvialClonotype in vignette
* Changed the alluvialClonotype assessment to account for only 1 condition


CHANGES IN VERSION 1.2.3
------------------------

* Changed the access of the sample data to github.io repo:
readRDS(url("https://ncborcherding.github.io/vignettes/scRepertoire_example.rds"))


CHANGES IN VERSION 1.2.2
------------------------

* Removed Startrac-based functions in order to pass build on Bioconductor.

DEPRECATED AND DEFUNCT

* Deprecate StartracDiversity()


CHANGES IN VERSION 1.2.0
------------------------

The first version of scRepertoire submitted to Bioconductor.

SIGNIFICANT USER-VISIBLE CHANGES

* Added support for SingleCellExperiement format.


DEPRECATED AND DEFUNCT

* Deprecate combineSeurat in favor or combineExpression().
* Deprecate seurat2List in favor of expression2List().
