version 0.1: (2015-04-20)

- Original release

version 0.1.1: (2015-04-21)

- Improved documentation

version 0.1.2: (2015-04-23)

- In 'BASiCS_Sim': change 'sum(phi)==n' by 'all.equal(sum(phi),n)'

version 0.1.3: (2015-05-18)

- 'plotBASiCSDispVsExp': 'log="xy"' argument added
- 'BASiCS_Data': internal checks added (pre-filter of samples and transcripts)
- 'BASiCS_MCMC' c++ code: Rcpp::checkUserInterrupt() added for fast 
user-requested interruption of MCMC sampler
- S4 method 'plot' for 'BASiCS_Chain' signature: argument 'Column' replaced by 
'Gene' and 'Cell'
- Replacement of 'plotBASiCSNormPhi' and 'plotBASiCSNormS' by S4 method 'plot' 
('BASiCS_Summary' signature)
- S4 method 'plot' for 'BASiCS_Summary' signature: does not include plots for 
all model parameters
- S4 method 'plot' for 'BASiCS_Summary' signature: does not include 
scatterplots of gene-specific and cell-specific model parameters (replacing 
'plotBASiCSExpVsDisp')
- 'BASiCS_VarianceDecomp' has been made visible to users (former 
'HiddenVarDecomp' function) and output does now allow gene annotation. 
- 'BASiCS_Filter' function added.
- Vignette has been updated according to the changes above. Instructions for 
installation were added. 
- 'BASiCS_Filter' function added.
- Dependency to R (>= 3.1.0) has been added.

version 0.1.4: (2015-05-21)

- 'BASiCS_Denoise' function added. It produces a table of normalised and 
denoised expression counts (after removing the effect of technical variation). 

version 0.1.5: (2015-05-27)
- Small typo in 'BASiCS_VarThresholdSearchHVG' and 
'BASiCS_VarThresholdSearchLVG' has been fixed. 

version 0.1.6: (2015-06-01)
- Replacement of parameter-specific 'displayChain's functions by a generic 
method displayChainBASiCS
- Replacement of parameter-specific 'displaySummary's functions by a generic 
method displaySummaryBASiCS
- In 'BASiCS_DetectHVG' and 'BASiCS_DetectLVG': constrain added to that 
prob >= 0.5 is required to detect HVG and LVG

version 0.2.0: (2015-06-24)
- New parametrization for mRNA content size factors $\phi_j$ that improves 
mixing of the MCMC algorithm (using adaptive Dirichlet proposals)
- Updated vignette

version 0.2.1: (2015-07-23)
- Argument 'GeneNames' has been added to functions 'BASiCS_VarianceDecomp', 
'BASiCS_DetectHVG', 'BASiCS_DetectLVG' so that users can specify gene labels 
or names that will be used for these functions's output. 

version 0.3.0: (2015-07-31)
- New slot BacthInfo in 'BASiCS_Data' class
- Batch-speficic technical variability parameters are allowed
- 'BASiCS_VarianceDecomp' modified to accommodate batch membership (including 
graphical output)

version 0.3.1: (2015-09-17)
- New slot GeneNames in 'BASiCS_Data' class
- Changes in the constructor `newBASiCS_Data` to allow easier construction of 
`BASiCS_Data` objects
- Minor changes to some functions' output to use the new GeneNames slot of 
'BASiCS_Data' class

version 0.3.2: (2015-10-23)
- Minor changes to the output of `BASiCS_MCMC` function (colnames of the 
elements related to the parameter $\theta$)
- Addition of extra optional parameter `ls.phi0` to `BASiCS_MCMC` function. 
This is helpful on situations where the default value led to slow mixing to 
the chains related to the normalising constants $\phi_j$'s. 

version 0.3.3: (2015-11-05)
- Same method as before but improved performance of C++ code

version 0.3.4: (2015-11-11)
- Fix of example code of 'newBASiCS_Data' function. Thanks to Simon Andrews 
for pointing out this issue.

version 0.3.5: (2015-11-27)
- Optional argument `PriorDelta` added to `BASiCS_MCMC` function, to allow 
optional use of `gamma` or `log-normal` priors for delta. 
- In `BASiCS_MCMC` function, change of default value of `s2.mu` to 0.5. Allows
better shrinkage in situations where a gene has zero counts across all cells.
- In `BASiCS_Data` class. Count matrices where a gene has zero counts across 
all cells are now allowed. However, a warning is returned in such case. 
Only use such matrices when running differential expression results. 

version 0.4.0: (2015-12-21)
- Preliminary functions for differential expression analyses (mean and 
over-dispersion) have been added. 

version 0.4.1: (2016-02-05)
- Fixed bug in vignette (usage of `newBASiCS_Data` function). Same bug has 
been fixed in documentation of class `BASiCS_Data`. 
- Optional argument 'Start' added to `BASiCS_MCMC` function to allow running 
chains with a variety of user-defined starting point. In general, we do not 
advise to use this argument as the default option has been tuned to 
facilitate convergence. 
- Updated documentation of 'BASiCS_DetectHVG' and 'BASiCS_VarianceDecomp' 
function (removing 'GeneNames' argument)
- Updated documentation for 'BASiCS_DV_TestDE' function. 
- Missing @description sections added to several .Rd files. 

version 0.5.0: (2016-03-03)
- Extended package description to include comparisons between pre-specified 
populations of cells
- `BASiCS_DV_Data`, `BASiCS_DV_Chain` and `BASiCS_DV_Summary` classes 
replaced by `BASiCS_D_Data`, `BASiCS_D_Chain` and `BASiCS_D_Summary` 
classes, respectively.
- Slot 'offset' added to `BASiCS_D_Chain` and `BASiCS_D_Summary` classes.
- Slot 'probHPD' added to `BASiCS_D_Summary` class. 
- Creation of `CombineBASiCS_Data` function to combine 2 independent 
`BASiCS_Data` objects into one `BASiCS_D_Data` object.
- Offset value added to the input of `show` method for `BASiCS_D_Chain` 
and `BASiCS_D_Summary` classes. 
- Creation of `CombineBASiCS_Chain` function to combine 2 independent 
`BASiCS_Chain` objects into one `BASiCS_D_Chain` object.
- 'GeneNames' slot added to `BASiCS_Data` class

version 0.5.1: (2016-03-07)
- In function `BASiCS_D_TestDE`. Probability threshold set to 0.95 
when EFDR fails to calibrate (simulations under the null)

version 0.5.2: (2016-03-07)
- In function `BASiCS_D_TestDE`. Probability threshold set to 0.90 
when EFDR fails to calibrate (simulations under the null)
- Fixed version number in description file.

version 0.5.3: (2016-03-09)
- Slots `BatchInfoTest` and `BatchInfoRef` added to `BASiCS_D_Data` class.
- `newBASiCS_D_Data` function modified to incorporate `BatchInfoTest` 
and `BatchInfoRef` slots.
- `CombineBASiCS_Data` function modified to incorporate `BatchInfoTest` 
and `BatchInfoRef` slots.
- `show` method for `BASiCS_D_Data` class modified to incorporate 
`BatchInfoTest` and `BatchInfoRef` slots.
- `GeneNames` argument missing in `makeExampleBASiCS_D_Data` has been added. 
- Slots `thetaTest` and `thetaRef` of `BASiCS_D_Chain` objects modified 
to accept matrices (necessary to allow multiple batches).

version 0.5.4: (2016-04-15)
- Minor fixes to the documentation files
- Argument `GenesSelect` was added to function `BASiCS_D_TestDE` to allow 
user-defined lists of genes to be included in the comparison between cell types. 

version 0.5.5: (2016-04-18)
- Small fix when checking the validity of a `BASiCS_D_Data` object. 
Thanks to Nils Eling. 
- Fixed issue with documentation files. 

version 0.5.6: (2016-04-19)
- Fixed message in `BASiCS_D_Test` function. This does not affect 
functionality. Only the message that is printed in the console.

version 0.5.7: (2016-04-27)
- Welcome message added

version 0.5.8: (2016-05-18) 
- After profiling of c++ functions, minor edits to improve memory usage. 
These do not affect user interface
- Small change in funtion 'makeExampleBASiCS_Data' to avoid 'NOTICE' message

version 0.5.9: (2016-05-19)
- Dependency to 'scran' added
- 'HiddenBASiCS_MCMC_Start' modified to use 'scran' estimates as starting 
values. This allows faster convergence.
- Updated 'README.md' file to build and access vignette during installation 

version 0.5.10: (2016-05-20)
- Updated bug in 'HiddenBASiCS_MCMC_Start' function (thanks to Joanna 
Dreux for noticing this issue)

version 0.5.11: (2016-05-24)
- 'importMethodsFrom(scran, computeSumFactors)' added to NAMESPACE

version 0.6.1: (2016-05-25)
- Argument 'WithSpikes' added to 'makeExampleBASiCS_Data', generating 
an example data with no spikes
- Modifications to validity checks of 'BASiCS_Data' class to allow no 
spikes case (SpikeInput = 1)
- 'show' methods for 'BASiCS_Data' class modified to deal with no spike case
- Checks for 'BASiCS_Data' object modified to require: either spikes or batches
- 'BASiCS_MCMC' modified for no spikes case (if/else statement only, 
not yet functional)
- 'HiddenBASiCS_MCMC_Start' modified for no spikes case
- Function 'HiddenBASiCS_MCMCcppNoSpikes' added. Update for 'phi' is pending. 
- Small vignette file for no spikes case added

version 0.6.2: (2016-05-31)
- Template for 'phiUpdateNoSpikes' has been added. 
- Minor change in 'phiUpdate' for all 'HiddenBASiCS_MCMCcpp' functions 
(to avoid re-writing phi0)
- Faster adaptation steps for 'HiddenBASiCS_MCMCcppBatch' 
'HiddenBASiCS_MCMCcppNoSpikes'
- 'HiddenBASiCS_MCMCcppNoSpikes' completed for testing stage 
(not ready for users)

version 0.6.3: (2016-05-31)
- Small update in wellcome message. 

version 0.6.4: (2016-06-01)
- Safety checks added to 'phiUpdateNoSpikes' 

version 0.6.5: (2016-06-8)
- Modified identifiability constrains for no spikes case.

version 0.6.6: (2016-07-27)
- First working version of no spikes case (constrained mu's)

version 0.6.7: (2016-07-28)
- Minor changes in the validity checks of 'BASiCS_D_Data' objects

version 0.6.8: (2016-07-28)
- Sequential updates for mu in MCMC (no spikes case only)

version 0.6.9: (2016-08-01)
- Dirichlet-based proposals for mu in MCMC (no spikes case only)

version 0.7.0: (2016-08-02)
- Sequential updates for mu in MCMC (no spikes case only)

version 0.7.1: (2016-08-05)
- Random reference in sequential updates for mu (no spikes case only)

version 0.7.2: (2016-08-05)
- Same as v 0.7.2 but more efficient

version 0.7.3: (2016-08-08)
- Reference set to be the gene closest to the average (no spikes case only)

version 0.7.4: (2016-08-09)
- Modified constrain to include 'expressed' genes only (no spikes case only)

version 0.7.5: (2016-08-10)
- Modified constrain to include 'expressed' genes only (no spikes case only)

version 0.7.6: (2016-08-11)
- As v 0.7.5 but with extra argument for constrain limit (no spikes case only)

version 0.7.7: (2016-08-12)
- ConstrainType = 3 implemented (no spikes case only)

version 0.7.8: (2016-08-15)
- ConstrainType = 4 implemented (no spikes case only)

version 0.7.9: (2016-10-31)
- C++ code cleaned regarding parameter updates (no spikes case)
- Updated email in description file and welcome message
- 'BASiCS_MCMC' modified so that "log-normal" is the default value 
for PriorDelta

version 0.7.10: (2016-10-31)
- Minor changes in 'BASiCS_MCMC' to have more meaningful variable names
- Minor changes in 'BASiCS_MCMC' to make no-spikes case functional 

version 0.7.11: (2016-10-31)
- Comments added to clarify no spikes case in 'BASiCS_MCMC' function. 

version 0.7.12: (2016-11-01)
- Change in defaul value of 'PriorDelta' (v 0.7.9) has been reverted 
for reproducibility issues. Message added to the start of the function 
so that users are aware of making the change. 
- PriorDelta = 'gamma' is now allowed for no spikes case

version 0.7.13: (2016-11-02)
- Typo on the arguments of 'HiddenBASiCS_MCMCcppNoSpikes' function has been 
fixed ('Constrain' instead of 'ConstrainType')
- Validity check '(y(i) > 1e-3)' moved later on in 'deltaUpdateNoSpikes' to 
avoid breaking the code when it is not really necessary!

version 0.7.14: (2016-11-03)
- Debug message removed from 'muUpdateNoSpikes' function. 

version 0.7.15: (2016-11-07)
- ConstrainType = 1 (untrimmed) re-introduced for no-spike case (illustration 
purposes only)
- RefGene removed from AR report
- Added console report of RefGene choice

version 0.7.16: (2016-11-07)
- ConstrainType = 3 (stochastic ref) re-introduced for no-spikes case

version 0.7.17: (2016-11-07)
- Error fixed in the definition of RefGenes

version 0.7.18: (2016-11-08)
- Function 'BASiCS_LoadChain' added to simplify the loading of 
pre-computed chains
- Imports from 'testthat' library added to NAMESPACE file
- Small changes in 'BASiCS_D' classes to allow offset

version 0.7.19: (2016-11-14)
- RefGene information to be stored as .txt file

version 0.7.20: (2016-11-14)
- 'newBASiCS_Data' function modified to allow no spikes case

version 0.7.21: (2016-11-15)
- 'ConstrainType' = 4, 5 added (exclude genes with capture in less than 
'ConstrainLimit'100% of the cells)

version 0.7.22: (2016-11-16)
- Fixed bug for 'ConstrainType' = 5 (affects no spike case only)

version 0.7.23: (2016-11-21)
- Cleaning-up of identifiability constrain options for the no spike case

version 0.7.24: (2016-11-23)
- Median changed to mean when calculating identifiability constrain for 
the no spike case

version 0.7.25: (2017-01-11)
- Fixed typo in vignette file (thanks to Dmitriy Zhukov for pointing this out)

version 0.7.26: (2017-02-09)
- Update of 'BASiCS_Filter' function to include a 'BatchInfo' argument 
(thanks to Dmitriy Zhukov for suggesting this)
- Vignette file updated accordingly.
- Update of 'newBASiCS_Data' function to prevent issues related to 
unused levels when the 'BatchInfo' argument is set as a 'factor' (thanks 
to Kevin Rue-Albrecht for pointing out this issue)

version 0.7.27: (2017-05-09)
- Bug fixed in 'BASiCS_Filter' function to stop the code crashing when there 
are genes with zero counts across all cells.

version 0.7.28: (2017-07-21)
- Fixed dependency to 'data.table' to prevent errors in 'BASiCS_LoadChain' 
function(thanks to Yongchao Ge for pointing out this issue). This change 
affects the DESCRIPTION file as well as the 'BASiCS_LoadChain' function. 

version 0.7.29: (2017-07-24)
- 'BASiCS:::HiddenBASiCS_MCMC_Start' function modified regarding the definition 
of starting values for mu (to avoid adding +1 when it's not necessary)
-  'BASiCS:::HiddenBASiCS_MCMC_Start' modified to have better starting values 
for delta (this is based on eq 2 from Vallejos et al, 2016)

version 0.7.30: (2017-07-26)
- Typo fixed in 'BASiCS:::HiddenBASiCS_MCMC_Start' function (thanks to 
@bdulken for pointing out this issue)

version 1.0.0: (2017-07-29)
- Initial big merge with @nilseling changes (in preparation for 
Bioconductor submission)
- For reference, here is a summary of the changes implemented by @nilseling:
  * Creation of individual .R for each R function (but all 'Hidden' functions 
  are in one file)
  * BASiCS_Data class replaced by SummarizedExperiment class (Bioconductor)
  * Contact email updated to 'cvallejos@@turing.ac.uk'
  * Methods for BASiCS_Data and BASiCS_D_Data objects removed (these classes 
  no longer exist)
  * Adjust newBASiCS_Data function to create a SummarizedExperiment object
  * 'cat' calls replaced by 'message' calls
  * Clean up of BASiCS_D_TestDE function (removed unused args)
  * Clean up of BASiCS_DetectHVG_LVG function (using SummarizedExperiment class)
  * Clean up of BASiCS_MCMC function (using SummarizedExperiment class)
  * Clean up of BASiCS_Sim function (using SummarizedExperiment class; 
  extra arg 'muSpikes')
  * Clean up of BASiCS_DetectHVG_LVG function (using SummarizedExperiment class)
  * Clean up of BASiCS_VarianceDecomp function 
  (using SummarizedExperiment class)
  * Clean up of BASiCS_VarThresholdSearchHVG function 
  (using SummarizedExperiment class)
  * Clean up of BASiCS_DenoisedCounts function 
  (using SummarizedExperiment class)
  * Clean up of BASiCS_DenoisedRates function (using SummarizedExperiment class)
  * Clean up of HiddenBASiCS_MCMC_Start function 
  (using SummarizedExperiment class)
  * Clean up of makeExampleBASiCS_Data function 
  (using SummarizedExperiment class) 
  * Removed methods associated to BASiCS_D_MCMC class (no longer in use)
  * NAMESPACE + Rd files updated accordingly
  * DESCRIPTION file updated accordingly
  * Vignette file updated accordingly
  
version 1.0.1: (2017-07-31)
- Minor changes function-by-function (revision of documentation + minor bugs)
  * newBASiCS_Data : added ref to GB paper + default par value doc + 
  Nils as author
  * BASiCS_Filter : added ref to GB paper + default par value doc 
  * makeExampleBASiCS_Data : added ref to GB paper + default par value doc + 
  Nils as author
  * BASiCS_MCMC : added ref to GB paper + Nils as author + fix print of 
  system.time + updated examples
- Major changes function by function
  * makeExampleBASiCS_Data : `Case1` param replaced by `Example` 
  (vignette + unit test updated accordingly)
  * BASiCS_MCMC : default value for PriorDelta set to 'log-normal' 
  * HiddenBASiCS_MCMC_Start : new starting values for delta (as in main repo)
  
version 1.0.2: (2017-08-01)
- Minor changes function-by-function (revision of documentation + minor bugs)
  * BASiCS_MCMC : 'MCMC_Output' replaced by 'Chain' in examples
- Major changes function-by-function
  * BASiCS_MCMC : chains stored a single .Rds files, with BASiCS_Chain format 
  (rather than separate .txt files)
  * BASiCS_LoadChain : updated accordingly
  * BASiCS_DetectHVG : evidence threhold to be defined by EFDR only 
- Vignette updated accordingly 

version 1.0.3: (2017-08-01)
- Minor changes function-by-function (revision of documentation + minor bugs)
  * BASiCS_DetectHVG / LVG: added vertical/horizontal lines in EFDR/EFND plot, 
  subtasks moved to hidden functions (avoids repeated code)
- Major changes function-by-function
  * BASiCS_DetectLVG : evidence threhold to be defined by EFDR only 
  * BASiCS_DetectHVG / LVG: fix on default prob threshold = 0.5 when optimal 
  is < 0.5
- Examples in BASiCS_MCMC updated accordingly
- Vignette updated accordingly

version 1.0.4: (2017-08-01)
- Minor changes function-by-function (revision of documentation + minor bugs)
  * BASiCS_VarThresholdSearchHVG / LVG : EFDR criteria updated as in 
  BASiCS_DetectHVG / LVG
  * BASiCS_TestDE : added examples
- Major changes function-by-function
  * BASiCS_D_TestDE : no longer in use message added
- Examples in BASiCS_MCMC updated accordingly
- Vignette updated accordingly
- Updated DESCRIPTION file (authors and description)
- Updated welcome message (with link to new wiki)

version 1.0.5: (2017-08-01)
- Major changes function-by-function
  * BASiCS_TestDE : plotting functionality for offset added
- ACF plot added to BASiCS_Chain plots

version 1.0.6: (2017-08-02)
- 'matrixStats' added within 'Imports' in DESCRIPTION (to use 
'colMedians' function)
- Minor changes function-by-function (revision of documentation + minor bugs)
  * BASiCS_TestDE : Improved offset plots
- Major changes function-by-function
  * BASiCS_TestDE : Ref/Test notation changed to Group1/2 + output table names 
  changed (to Mean/Disp) + 
  offset corrected objects as output + separated output tables Mean/Disp + post 
  prob threshold moved to hidden function (avoids duplicated code)
  
version 1.0.7: (2017-08-03)
- Multiple changes in BASiCS_TestDE:
  * Added examples of table viewing in doc
  * Added chain extracts to run examples
  * Results for differential dispersion to exclude differential mean genes
  * EFDR / EFNR control plot added
  * MA plots added
- Main hidden functions moved into individual files
- 'graphics' + 'KernSmooth' added as dependence to use 'smoothScatter'
- 'smooth' argument changed to 'SmoothPlot' in plot functions/methods
- Added reference :: to basic functions (e.g. boxplot, var, acf, etc)
- devtools::check() OK - 1 warning : BiocStyle in vignette

version 1.0.8: (2017-08-03)
- 'Data' arg removed from args in:
  'HiddenHeaderDetectHVG_LVG' + 'HiddenVarDecomp' + 'BASiCS_DetectHVG' + 
  'BASiCS_DetectLVG' + 'BASiCS_VarThresholdSearchHVG' + 
  'BASiCS_VarThresholdSearchLVG'
- 'object' arg renamed as 'Chain' in 'BASiCS_DetectHVG' + 'BASiCS_DetectLVG' 
  + 'BASiCS_VarThresholdSearchHVG' + 'BASiCS_VarThresholdSearchLVG'
- Examples in BASiCS_MCMC updated to use built-in chain
- Removal of 'smoothPlot' usage in plots for 'BASiCS_Summary' class (avoids 
issues with log)
- Volcano plots added in BASiCS_TestDE function
- Resolved issues with log scale in 'smoothScatter'
- Minor bugs fixed in BASiCS_TestDE
- 'EviThreshold' arg replaced by 'ProbThreshold' in 'BASiCS_HVG' + 'BASiCS_LVG'
- Vignette updated accordingly

version 1.0.9: (2017-08-04)
- newBASiCS_Data : added check to ensure SpikeInfo is a data.frame
- BASiCS_TestDE : default value for EpsilonM & EpsilonD has changed
- Vignette + examples updated accordingly

version 1.0.10: (2017-08-06)
- BASiCS_TestDE : changes in output messages
- Gene name added in plot method for BASiCS_Chain objects

version 1.0.11: (2017-08-06)
- BASiCS_VarianceDecomp : small bugs fixed (unused Data object)
- colnames fixed on cell-specific slots ChainSC and ChainRNA
- Rcpp::checkUserInterrupt() activated in C++ code for interruptions
- 'grDevices' added as dependency

version 1.0.11: (2017-08-13)
- 'WithSpikes' argument removed from 'BASiCS_LoadChain' function

version 1.0.12: (2017-08-14)
- 'SummarizedExperiment' class replaced by 'SingleCellExperiment'
- Updated vignette

version 1.0.13: (2017-08-15)
- Minor changes to documentation
- Minor changes to vignette

version 1.1.0: (2017-08-16)
- Minor changes required to pass BiocCheck (used formatR and BiocChecks)

version 0.99.0: (2017-08-28)
- Minor changes to complete Bioconductor submission checklist
- Version re-numbered according to Bioconductor guidelines

version 0.99.2: (2017-09-18)- After @nturaga review
- 'newBASiCS_Data': format + checks moved to `HiddenChecksBASiCS_Data` function
- `HiddenChecksBASiCS_Data`: use of colMeans2, rowMeans2
- Format in welcome message
- 'newBASiCS_Chain': format 

version 0.99.3: (2017-09-21)

- Extra unit test (parameter estimates for a given seed)
- Format + vectorisation in `HiddenThresholdSearchTestDE` function
- `HiddenProbDE` removed as no longer needed
- Additional unit test for differential test added
- Format for `BASiCS_TestDE` function 
- Format for `HiddenBASiCS_MCMC_Start` function
- Format for `HiddenChecksBASiCS` function
- Format for `BASiCS_D_TestDE`
- Format for all S4 methods

version 0.99.3: (2017-09-21)

- 2^ added to FC in `BASiCS_TestDE` TableDisp
- Format for data documentation
- Format for classes definition
- Format + vectorization for `BASiCS_Filter`
- Format for `BASiCS_LoadChain`

version 0.99.3: (2017-09-22)

- Removal of second example in `makeExampleBASiCS_Data` (no longer
required due to DataSC, DataRNA)
- Format for `makeExampleBASiCS_Data`
- Format for `BASiCS_Sim`

version 0.99.3: (2017-09-22)

- Format + matrixStats usage in `BASiCS_VarianceDecomp`
- Unit test for HVG/LVG detection added
- Minor bug in `BASiCS_TestDE` resolved (related to colMeans2 use)
- Format + matrixStats usage in `HiddenVarDecomp`
- `message` replaced by `cat` in Methods.R
- Removal of no-longer-needed Hidden functions
- Format in `HiddenHeaderDetectHVG_LVG`
- Format in `HiddenPlot1DetectHVG_LVG` + `HiddenPlot2DetectHVG_LVG`
- Format + matrixStats usage in `BASiCS_DetectHVG` + `BASiCS_DetectLVG`
- Format in `BASiCS_VarThresholdSearchHVG`
- Format in `HiddenThresholdSearchDetectHVG_LVG`

version 0.99.3: (2017-09-22)

- Calculations in `BASiCS_DenoisedRates` moved to C++ to increase speed

version 0.99.3: (2017-09-24)

- Format in `BASiCS_DenoisedCounts`
- Edits in `HiddenBASiCS_MCMCcpp` and associated C++ functions
  * Dimensions for mu storage upto q0 only
  * Creation of generic storage values
  * Formating of long lines
  * Removal of no-longer-required functions and debug lines

version 0.99.3: (2017-09-25)
- Edits in `HiddenBASiCS_MCMCcpp` and associated C++ functions
  * Optimization of MH updates

version 0.99.3: (2017-09-25)
- Edits in `HiddenBASiCS_MCMCcpp` and associated C++ functions
  * Batch & no-batch versions merged in a single function
  * Avoids double transponse for chain storage
  
version 0.99.4: (2017-09-25)
- Format in `BASiCS_MCMC`
- Minor bug fixed in `BASiCS_DetectLVG` plots
- Added examples in `BASiCS_DenoisedCounts` + `BASiCS_DenoisedRates`
- Removal of `Example` argument in `makeExampleBASiCS_D_Data`
- Format in vignette
- R CMD CHECK passed
- R CMD BiocCheck passed
  
version 0.99.5: (2017-09-26)  
- Change of default `PriorDelta` value in `BASiCS_MCMC` 
- Unit tests modified accordingly

version 0.99.7: (2017-10-05) - After @nturaga review
- `inst` folder has been deleted
- Removal of `...` arg in `segments` - `plot` method for `BASiCS_Summary`

version 0.99.8: (2017-10-10)
- version bump to trigger a new Bioconductor build

version 0.99.9: (2017-10-16)
- Updated URL and BugReports in DESCRIPTION

version 0.99.10: (2017-10-17)
- Updated README with BioC installation instructions and @nturaga acknowledgment

version 0.99.12: (2017-10-17) 
- Update of NEWS with changes by @neling 
- Small typo fix in class validity from @neling last commit
- Changes in `BASiCS_Chain` and `BASiCS_Summary` classess to contain a single 
`list` slot where all parameters are stored. This allows greater flexibility 
to incorporate ongoing developments of BASiCS but does not affect user interface. 
- `BASiCS_DenoisedCounts`, `BASiCS_DenoisedRates`, `BASiCS_DetectHVG`, 
`BASiCS_DetectLVG`, `BASiCS_MCMC`, `BASiCS_TestDE`, `HiddenVarDecomp`, 
`newBASiCS_Chain` functions and all methods updated accordingly 
- `ChainSC` and `ChainRNA` example objects updated accordingly
- Unit tests updated accordingly
- Wiki page updated accordingly
- `updateObject` generic method imported from `BiocGenerics` 
- New generic methods definition moved to AllGenerics.R
- Change in class definition to store current packageVersion
- `BASiCS_LoadChain` function updated to deal with old class definition and
.txt storage.
- Shorter welcome message. 
- Sanity checks in `BASiCS_TestDE` moved to separate file. 
- Updated code indentation in `BASiCS_TestDE`
- Warning in `BASiCS_DetectHVG` and `BASiCS_DetectLVG` when user provides
posterior probability thresholds as input
- Unused argument removed from `HiddenEFDR` and `HiddenEFNR` functions
- Minor changes to pass R CMD check
- Check library passes R CMD BiocCheck
- Tidy up NAMESPACE
- Tidy up NEWS
- Merge Devel_class into master branch

version 0.99.13: (2017-10-17)  
- @neling email added to DESCRIPTION + author contributions
  
version 0.99.14: (2017-10-19) 
- Added checks to ensure input `SingleCellExperiment` object has all info

version 1.0.1: (2018-03-18) - build error fix
- New unit tests (more modular): example data, starting values MCMC, MCMC 
sampler for fixed starting values 