NEWS

---

BASiCS 2.15.4 (2024-03-25)

• Minor bug fixe in the 'subset' method for 'BASiCS_Chain' objects

BASiCS 2.15.2 (2023-12-22)

• Minor bug fixes

BASiCS 2.13.5 (2023-09-20)

• Minor update in no-spikes code to avoid re-calculating a constant quantity. Does not affect output.

BASiCS 2.13.3 (2023-06-16)

• Reverts 'LazyData' to 'false' based on BiocCheck feedback

BASiCS 2.13.2 (2023-06-16)

• Changes 'LazyData' to 'true' to avoid errors

BASiCS 2.13.1 (2023-06-16)

• Fixes error in tests associated to the behaviour of 'matrixStats::colMedians'

BASiCS 2.11.9 (2023-03-07)

• Fixes minor bug in test_denoised.R

BASiCS 2.11.8 (2023-03-07)

• fixes conflict after merge and version bump only

BASiCS 2.11.7 (2023-03-07)

• Updates NEWS
• version bump to trigger new build
• Fixes small bugs in tests (test_misc.R and test_divide_and_conquer.R)
• Minor changes suggested by BiocCheck

BASiCS 2.11.6 (2023-02-07)

• Adds 'BASiCS_CalculateERCC()' to NAMESPACE
• Creates unit test for 'BASiCS_CalculateERCC()'

BASiCS 2.11.5 (2023-01-04)

• Changes maintainer
• Remove unicode mu in documentation

BASiCS 2.11.4 (2022-12-15)

• Solves bug in 'BASiCS_DiagPlot()'

BASiCS 2.11.3 (2022-12-15)

• Creates 'BASiCS_CalculateSpikeIns()' to perform spike-in calculation (depends on the 'scRNAseq' package).
• Adds extra option to plotting functions for MCMC diagnostics (e.g. 'BASiCS_DiagPlot()')

BASiCS 2.11.2 (2022-11-23)

• Bugfix in DetectLVG/HVG, see Issue #265; delta column in results was actually duplicated mu column.
• Change BASiCS_CorrectOffset to also alter the scale of the normalisation factors when WithSpikes=FALSE.
• Add "rhat" option to BASiCS_DiagHist and BASiCS_DiagPlot

BASiCS 2.9.7 (2022-09-06)

• Bugfix in BASiCS_DetectHVG/BASiCS_DetectLVG.

BASiCS 2.9.6 (2022-09-05)

• Add TransLogit parameter to BASiCS_PlotDE to have volcano plots on a logit scale. As the posterior probabilities are in the interval [0, 1] this may make it easier to visualise difference in "interesting" regions (e.g., 0.6-1)

BASiCS 2.9.5 (2022-07-29)

• Further bugfix in subset method for BASiCS_Chain objects. subset now respects the ordering implied by character or numeric indices, where it previously did not.

BASiCS 2.9.4 (2022-07-28)

• Update roxygen version

BASiCS 2.9.3 (2022-07-18)

• Bugfix for divide and conquer code - handle arguments like StoreChains and RunName correctly in this context.

BASiCS 2.9.2 (2022-07-18)

• Implement parallel tests
• Remove variance decomp plotting code from an internal code block to the public BASiCS_PlotVarianceDecomp.

BASiCS 2.9.1 (2022-05-04)

• switch from using DOUBLE_EPS to a function call to std::numeric_limitsdouble::epsilon() - credit Tomas Kalibera for informing by private correspondence.

BASiCS 2.7.4 (2022-02-22)

• Bugfixes in the subset method for BASiCS_Chain objects.

BASiCS 2.7.1 (2021-11-03)

• Add FixNu argument to fix scaling parameters to scran normalisation factors when WithSpikes=FALSE
• Exclude features with absolute estimates of fold change/difference less than the DE threshold when performing differential expression analysis with BASiCS_TestDE.

BASiCS 2.5.7 (2021-10-05)

• Fix tests for BiocParallel behaviour.

BASiCS 2.5.6 (2021-10-05)

• Revert 2.5.5 changes; add expectation to empty tests.

BASiCS 2.5.5 (2021-08-24)

• Bugfix tests with change in BiocParallel behaviour

BASiCS 2.5.4 (2021-08-24)

• Ensure ordering of genes in chains is consistent with input data when using divide and conquer

BASiCS 2.5.3 (2021-08-11)

• Add GeneExponent and CellExponent settings for divide and conquer.

BASiCS 2.5.2 (2021-08-11)

• Add better spacing around EFDR message.
• Fix ggplot2 'guide=FALSE' warnings
• Remove an errant browser() call

BASiCS 2.5.1 (2021-05-19)

• Add error condition for unnamed cells.

BASiCS 2.3.4 (2021-04-18)

• Add missing import from scran

BASiCS 2.3.3 (2021-04-14)

• Version bump to trigger new build

BASiCS 2.3.2 (2021-04-14)

• Bug fixes in handling of divide and conquer inference.

BASiCS 2.3.1 (2020-12-14)

• scaling of 'mu.mu' in '.EmpiricalBayesMu' to match the scale given by spike-ins
• scaling of 'mu0' in '.BASiCS_MCMC_Start' to match the scale given by spike-ins when using an EB prior for mu
• lower minimum tolerance 'mintol_mu' (1e-5 instead of 1e-3) as a default value in '.BASiCS_MCMC_ExtraArgs'

BASiCS 2.1.16 (2020-10-22)

• Updates '.BASiCS_MCMC_Start' to use different starting values when an empirical Bayes prior is assigned to mu
• Adds 'log_scale' parameter to '.EmpiricalBayesMu'
• Fixes small bug in '.BASiCS_MCMC_Start'
• Updates unit tests linked to the change in '.BASiCS_MCMC_Start'
• Adds fixed seeds to 'test_divide_and_conquer.R'

BASiCS 2.1.14 (2020-10-08)

• Add support for divide and conquer inference with 'BASiCS_DivideAndConquer' function. Add support for this function to 'BASiCS_MCMC'
• Add 'BASiCS_MockSCE' function to create a SingleCellExperiment object with arbitrary dimensions.
• Fix Makevars warning relating to PKG_CXXFLAGS

BASiCS 2.1.13 (2020-10-05)

• Add PriorParam argument to 'BASiCS_MCMC'

BASiCS 2.1.12 (2020-10-01)

• Remove unused DelayedArray call from tests

BASiCS 2.1.11 (2020-09-30)

• Updated documentation for 'Threads' in 'BASiCS_MCMC' to indicate default value.

BASiCS 2.1.10 (2020-09-30)

• Documents 'Threads' argument.

BASiCS 2.1.9 (2020-09-28)

• Add 'Threads' argument to 'BASiCS_MCMC', allowing parallelisation of MCMC updates across cells or genes using openMP.
• Reduce BatchInfo requirement for no spikes sampler to a warning, from an error.

BASiCS 2.1.8 (2020-09-28)

• Minor edit in the vignette to recommend the use of a seed for reproducible results when using 'BASiCS_MCMC'.

BASiCS 2.1.7 (2020-09-23)

• Bugfix in format method for ResultVG class.
• For 'BASiCS_PlotDE', if only one plot is produced, the plot is returned as a bare ggplot object rather than using 'cowplot::plot_grid'
• Added 'EpsilonThreshold' argument for 'BASiCS_DetectHVG' and 'BASiCS_DetectLVG'. This uses a threshold on epsilon values to identify LVGs and HVGs. Also adds a 'MinESS' argument to 'BASiCS_DetectHVG' and 'BASiCS_DetectLVG'.
• Deprecated 'newBASiCS_Data' and the 'format' methods for Results classes. For the latter, use 'as.data.frame' instead.
• Improved documentation for BASiCS_ResultVG class
• 'BASiCS_MCMC' now computes and stores ESS as an attribute of parameter matrices when sampling has completed.
• Make use of Parameter argument consistent across several methods, where Param and Which were used before.
• Extended BASiCS_DiagPlot to enable other diagnostic measures
• Moved to store molecule counts in 'rowData(altExp(sce))' rather than 'metadata(sce)'
• Remove dependency to KernSmooth
• Set some values to NA if they relate to genes captured in < 2 cells
• Add option to exclude spike-ins in 'BASiCS_DenoisedCounts'. Also use a slightly more principled calculation internally.
• See issues #182, #39, #91, #169, #181, #178, #202, #190, #173

BASiCS 2.1.6 (2020-08-05)

• Prevents usage of 'BASiCS_VarThresholdSearchVG' when using residual overdispersion parameters

BASiCS 2.1.5 (2020-08-05)

• Minor change on the definition of 'OrderVariable' within 'BASiCS_DetectVG'

BASiCS 2.1.4 (2020-08-05)

• Extended unit tests to verify the validity of input parameters for 'BASiCS_DetectLVG' and 'BASiCS_DetectHVG'.
• Updated documentation for 'BASiCS_DetectVG' to account for new default values and the type of output (now object with class 'BASiCS_ResultVG').
• Unit tests for LVG updated as new default value for 'ProbThreshold' is used whenever the EFDR calibration fails (2/3 as opposed to 0.5).
• Minor changes in 'BASiCS_VarThresholdSearch' to avoid errors in the presence or absence of epsilon. This function is likely to be deprecated.
• Updates default probability threshold in '.ThresholdSearch' when EFDR calibration fails. This is now set to 'ProbThreshold' (not 0.9)

BASiCS 2.1.3 (2020-07-29)

• New default values for 'PercentileThreshold' (= NULL), 'VarThreshold' (= NULL) and 'ProbThreshold' (= 2/3) in 'BASiCS_DetectVG'). The latter is compatible with the default values in 'BASiCS_TestDE'.
• Changes default behaviour of 'BASiCS_DetectLVG', 'BASiCS_DetectHVG' in accordance with the changes introduced for 'BASiCS_DetectVG'.

BASiCS 2.1.2 (2020-07-29)

• Moves auxiliary functions related to HVG/LVG analysis to 'utils_VG.R'. This includes '.VGPlot', '.VGGridPlot', '.HeaderDetectHVG_LVG' and '.VG'.
• Updated warning messages in '.HeaderDetectHVG_LVG'
• Updated rules for 'EFDR' and 'ProbThreshold' parameters in 'BASiCS_DetectVG'. If 'EFDR = NULL', EFDR calibration is not used and posterior probability threshold is set to be equal to 'ProbThreshold'. This behaviour is consistent with the rules used in 'BASiCS_TestDE'.
• Creates '.CheckProbEFDR' to perform validity checks for 'ProbThreshold' and 'EFDR' in all tests (HVG/LVG and DE).
• Cleans code within '.ThresholdSearch' and 'BASiCS_DetectVG'
• Removes 'Threshold' from the output provided by 'BASiCS_DetectVG'
• Removes duplicated plotting code in 'BASiCS_DetectVG'. Now calls 'BASiCS_PlotVG'.
• Changes '.VGGridPlot' and '.VGPlot' to use 'ggplot2:theme_classic()'

BASiCS 2.1.1 (2020-07-28)

• Bugfix in BASiCS_DetectHVG and BASiCS_DetectLVG. Epsilon/Delta,Sigma values were erroneously not returned.
• More detailed colouring of differential expression plots.
• Bugfix in labels for DE plots.

BASiCS 2.0.0 (2020-04-01)

• Improve UI for BASiCS_TestDE BASiCS_TestHVG/BASiCS_TestLVG and related functions by creating classes. Usage of objects documented in vignette.
• Reduce code duplication and refactor plots to use ggplot2.
• Add rudimentary unit tests for loading and some class methods. Fix several minor bugs.
• Change barplot in variance decomposition function to use ggplot2.

BASiCS 1.99.1 (2020-04-14)

• Minor change in documentation of 'BASiCS_VarianceDecomp' to use 'ggplot2' as reference link (instead of 'RColorBrewer')

BASiCS 1.99.0 (2020-04-07)

• Minor changes in vignette to increase figure sizes
• Version number updated to follow Bioc guidelines

BASiCS 1.9.26 (2020-03-25)

• Bugfix in BASiCS_Sim

BASiCS 1.9.25 (2020-03-13)

• 'ConstrainType' deprecated within 'BASiCS_MCMC' (internal option only)
• In 'tests_mcmc_arguments.R', adds 'set.seed' to avoid random failure of 'makeExampleBASiCS_Data'

BASiCS 1.9.24 (2020-03-13)

• Removes R from Depends in DESCRIPTION.
• Minor fix in the documentation of 'BASiCS_PriorParam' to pass BiocCheck.

BASiCS 1.9.23 (2020-03-10)

• Adds 'BASiCS_PriorParam' function. This function makes it easier to alter parameters for the prior distributions used in BASiCS. See issue #154.
• Adds RBFMinMax argument to 'BASiCS_PriorParam', which controls whether RBF are set at the minimum and maximum starting mu values.
• Adds MinGenesPerRBF argument to 'BASiCS_PriorParam'. This controls the minimum number of genes between around the centre of each RBF.

BASiCS 1.9.22 (2020-03-09)

• Bugfix in plot method when Param="sigma2"

BASiCS 1.9.21 (2020-03-05)

• Minor fix in 'BASiCS_MCMC' to fix warning (definition of 'PriorMu')

BASiCS 1.9.20 (2020-02-16)

• Fix bug in handling of tail probability tests that meant probabilities were not calculated correctly when Epsilon* = 0.

BASiCS 1.9.19 (2020-02-16)

• Adds a while loop in BASiCS_Sim to ensure it doesn't fail if some generated cells have zero counts.

BASiCS 1.9.18 (2020-02-16)

• Merges empirical Bayes changes with those from divide-and-conquer
• Minor changes in unit tests to account for empirical Bayes prior ( taking ParamPrior$mu.mu as a vector, rather than a scalar)

BASiCS 1.9.17 (2020-02-16)

• Implementation of empirical Bayes (EB) approach for 'mu' in 'BASiCS_MCMC'
• Additional parameter 'PriorMu' incorporated to 'BASiCS_MCMC'. This enables internal calculation of the EB prior.
• Creates '.EmpiricalBayesMu' to derive EB prior for mu.
• 'HiddenBASiCS_MCMC_InputCheck', 'HiddenBASiCS_MCMC_GlobalParams' and 'HiddenBASiCS_MCMC_ExtraArgs' renamed as '.BASiCS_MCMC_InputCheck', '.BASiCS_MCMC_GlobalParams' and '.BASiCS_MCMC_ExtraArgs'.
• Fixes minor bug in '.EmpiricalBayesMu'
• Fixes EB approach for no-spikes case (regression and no regression)
• Updates documentation of 'BASiCS_MCMC' to include 'PriorMu' as a parameter
• Removes dependency to 'scater' functions in '.EmpiricalBayesMu'.

BASiCS 1.9.16 (2020-02-16)

• Adds extra line in 'test_sim.R' to avoid warning in BiocCheck

BASiCS 1.9.15 (2020-02-16)

• Use expect_equal in scran test (now all suitable tests)
• Minor change in 'test_differential_test_reg.R' to use 3 instead of 2 decimal points. This hopefully avoids issues associated to a bug in 'round'. For details see: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17668

BASiCS 1.9.14 (2020-02-10)

• Changes coda::effectiveSize for a more efficient internal implementation.
• Adds 'CheckESS' and 'MinESS' arguments to 'BASiCS_TestDE' to filter genes for differential expression testing based on effective sample size.

BASiCS 1.9.13 (2020-02-05)

• Adds option for prior scaling parameters (relevant for new divide and conquer approach only; does not affect UI)

BASiCS 1.9.12 (2020-01-17)

• Fixes bug in 'BASiCS_CorrectOffset' for no-spikes case

BASiCS 1.9.11 (2020-01-11)

• Add unit tests for each MCMC update.

BASiCS 1.9.10 (2019-12-13)

• Further clean up in 'BASiCS_TestDE'. Creates new internal functions to avoid duplicated code across different tests: '.TestResults', '.ShowTestResults'

BASiCS 1.9.9 (2019-12-12)

• Version bump after pull request merge
• R version requirement set to 3.6.0
• 'dimnames<-' added for 'BASiCS_Chain' objects
• Additional input checks for 'BASiCS_DenoisedCounts' and 'BASiCS_DenoisedRates'

BASiCS 1.9.8 (2019-12-12)

• Clean-up for 'HiddenTailProbTestDE' -> renamed as '.TailProb'. Similar for '.ThresholdSearch', '.EFDR' and '.EFNR'
• Extra unit test for 'GenesSelect' parameter in 'BASiCS_TestDE'
• Removes 'HiddenThresholdSearchDetectHVG_LVG' as no longer needed.
• Changes in 'BASiCS_DetectHVG' and 'BASiCS_DetectLVG' to reuse same hidden functions as in 'BASiCS_TestDE' (extra potential changes exist)

BASiCS 1.9.7 (2019-12-05)

• Fixes bug in mu updates (log(mu) - mu.mu, rather than log(mu - mu.mu)). This does not affect default prior, only empirical Bayes approach.

BASiCS 1.9.6 (2019-12-04)

• Minor changes in 'test_misc.R' to expose hidden functions

BASiCS 1.9.5 (2019-12-04)

• Optional parameter added to all mcmc samplers to enable user-defined prior mean for log(mu).
• Requirement of R (>= 4.0.0) added as suggested by BiocCheck

BASiCS 1.9.4 (2019-12-04)

• Example chain objects updated to satisfy identifiability constrain
• 'test_vardecomp.R' updated accordingly

BASiCS 1.9.3 (2019-12-04)

• Introduces 'BASiCS_Draw' to enable synthetic data generation based on a 'BASiCS_MCMC' object (similar to splatter)
• Style changes to 'newBASiCS_Data'
• Changes in 'test_data_examples.R' to cover all cases.

BASiCS 1.9.2 (2019-12-04)

• Adds 'LazyData: true' in DESCRIPTION to pass R CMD Check (R-devel requirement)
• Updates 'BASiCS_LoadChain' to remove dependency to 'data.table'
• Alan added to README.md. Funding acknowledgement updated.

BASiCS 1.9.1 (2019-11-28)

• In 'HiddenBASiCS_MCMC_Start', 'scran::computeSumFactors' was replaced by 'scran::calculateSumFactors' in order to match new version of 'scran'.

BASiCS 1.7.20 (2019-10-17)

• Bumps version number to trigger new build.

BASiCS 1.7.19 (2019-10-08)

• BASiCS_TestDE now checks to ensure that both input chains have been run with Regression = FALSE or both with Regression = TRUE.
• Remove duplicated text from ‘BASiCS_Chain'’s show method.

BASiCS 1.7.18 (2019-10-06)

• Refactor HVG/LVG plots code to use 'ggplot2'. When calling 'BASiCS_DetectHVG' or 'BASiCS_DetectLVG', the plots are now stored in the returned list in the named element 'Plots'. The vignette has been updated to show the usage of this functionality.
• In all unit tests: use ‘expect_equal(foo, bar)' instead of 'expect_true(all.equal(foo, bar))'. This gives better printing (ie, if it’s not true it tells by what margin)
• Rename some functions for consistency in capitalisation. For example, 'BASiCS_showFit' has been deprecated and renamed to 'BASiCS_ShowFit'.
• Add a 'Smooth' argument to 'BASiCS_DiagPlot'.
• BASiCS_TestDE is now explicit about requiring the same number of samples in both chains. Previously it would fail due to arrays of non-conformable dimensions.
• Add some internal utility functions.
• Remove exportPattern("^[^\\Hidden]") meaning functions must be explicitly exported using roxygen tags.

BASiCS 1.7.17 (2019-10-04)

• Minor change in 'newBASiCS_Data' to avoid missing 'colnames' when adding 'colData'
• New unit test to verify that 'colnames' are not lost

BASiCS 1.7.16 (2019-10-04)

• Minor changes to NAMESPACE to pass R CMD Check

BASiCS 1.7.15 (2019-09-30)

• Swtich from 'matrixStats' dependency to 'Matrix' as it supports more general input classes (including sparse matrices)
• 'newBASiCS_Data' now requires input counts to be a 'matrix'.

BASiCS 1.7.14 (2019-09-27)

• Changed internal functions from 'matrixStats' to 'Matrix' to support more classes of matrix (eg, 'dgCMatrix'). BASiCS_MCMC now supports DelayedArray, dgEMatrix, dgCMatrix objects and likely more.

BASiCS 1.7.13 (2019-09-25)

• Updated unit tests to account for new default choice for 'min.mean' parameter in 'scran::computeSumFactors'
• New unit test to check for changes in 'scran::computeSumFactors'

BASiCS 1.7.12 (2019-09-15)

• changes maintainer's email address

BASiCS 1.7.11 (2019-09-15)

• 'Uncertainty' parameter added to 'BASiCS_showFit'. This enables optional inclusion of uncertainty measure around the regression trend.
• Re-ordering of parameter in c++ MCMC samplers (does not affect output)
• Avoid unnecessary transformations between NumericMatrix/Vector and arma::
• Removes 'isSpike' usage in 'BASiCS_Sim' documentation
• Removes 'isSpike' call from the vignette
• Adds missing parameters to the documentation of 'BASiCS_CorrectOffset'

BASiCS 1.7.10

• 'metadata(Data)$SpikeInput' is now required to be a 'data.frame'. This allows us to verify the correct order in spike-in inputs when the user manually modifies an existing 'SingleCellExperiment' object.
• Additional changes in 'newBASiCS_Data', 'HiddenBASiCS_MCMC_InputCheck', 'HiddenChecksBASiCS_Data' to avoid errors.
• 'HiddenBASiCS_MCMC_Start', 'HiddenBASiCS_MCMC_GlobalParams', 'BASiCS_DenoisedCounts' and 'BASiCS_DenoisedRates' modified to replace 'isSpike' by 'altExp'
• Some unit tests adapted accordingly

BASiCS 1.7.9 (2019-09-05)

• 'newBASiCS_Data', 'HiddenBASiCS_MCMC_InputCheck', 'HiddenChecksBASiCS_Data' and 'BASiCS_MCMC' modified to replace 'isSpike' by 'altExp'
• WIP - unit test do not pass

BASiCS 1.7.8 (2019-08-20)

• 'min.mean' parameter exposed in 'BASiCS_CorrectOffset' and 'BASiCS_TestDE'

BASiCS 1.7.7 (2019-08-20)

• Preliminary version of 'BASiCS_CorrectOffset' has been added. This includes a trimmed option for the offset calculation that excludes lowly expressed genes. This is similar to what is implemented in 'scran:::.rescale_clusters

BASiCS 1.7.6 (2019-08-19)

• Offset correction within 'BASiCS_TestDE' modified to use 'rowMedians' instead of 'rowSums2'. This makes it more robust to outlier genes.
• Unit tests updated accordingly.

BASiCS 1.7.5 (2019-07-30)

• Returns to original updates for X (fixed after burn-in)

BASiCS 1.7.4 (2019-07-30)

• Show method for regression objects now correctly shows number of cells.
• 'HiddenBASiCS_MCMCcppReg' and 'HiddenBASiCS_MCMCcppRegNoSpikes' (C++ code) modified to update design matrix throughout MCMC (GRBF locations remain fixed after the burn-in period is over)
• Unit tests updated accordingly.

BASiCS 1.7.3 (2019-07-29)

• Minor typo fixed in 'BASiCS_MCMC'.

BASiCS 1.7.2 (2019-07-28)

• Specific minimum tolerance thresholds (e.g. 1e-3 for mu updates) replaced by global parameters (e.g. 'mintol_mu'). Optional parameters; internal use only. Incorporated within 'HiddenBASiCS_MCMC_ExtraArgs'.
• General clean up to remove code redundancy in 'BASiCS_MCMC'
• 'HiddenBASiCS_MCMC_GlobalParams' created to facilitate clean-up above

BASiCS 1.7.1 (2019-07-27)

• 'is_true' deprecated in 'testthat'. Unit tests updated to use 'expect_true'

BASiCS 1.5.34 (2019-04-20)

• Fixes typo in vignette

BASiCS 1.5.33 (2019-04-19)

• Updated ERCC formula in the vignette.

BASiCS 1.5.32 (2019-04-17)

• Minor change in 'BASiCS_MCMC' to avoid storing adaptive variances in the 'BASiCS_Chain' object when 'StoreAdapt = TRUE'.
• New unit test to ensure the correct output in 'BASiCS_Chain@parameters'
• Minor change in 'Summary' method for 'BASiCS_Chain' class to avoid calculating posterior summaries when 'designMatrix' is part of the 'parameters' slot
• Added 'return' to the docummentation of 'BASiCS_effectiveSize'.

BASiCS 1.5.31 (2019-04-15)

• Updated vignette to include ERCC calculation

BASiCS 1.5.30 (2019-04-11)

• ‘BASiCS_effectiveSize' has been created as a wrapper of 'coda::effectiveSize'. This is to resolve issues when 'Param = ’epsilon'' as it contains 'NA' for very lowly expressed genes that are excluded from the mean/over-dispersion trend.

BASiCS 1.5.29 (2019-04-10)

• Unit test associated to 'BASiCS_Sim' updated to use a fixed seed and to check exact values being reproducible

BASiCS 1.5.28 (2019-04-09)

• Edited version of 'BASiCS_Sim' to allow no spikes and multiple batches
• Documentation updated accordingly

BASiCS 1.5.27 (2019-04-08)

• Edits ‘BASiCS_TestDE' to avoid low posterior probability thresholds derived from the EFDR calibration. This alters some of the related ’Hidden' functions.
• In 'BASiCS_TestDE', default values for 'EFDR_M', 'EFDR_D' and 'EFDR_R' were changed to 0.05.
• Unit tests updated accordingly

BASiCS 1.5.26 (2019-04-08)

• Similar changes applied to 'utils_MCMCcppReg.cpp' and 'utils_MCMCcppRegNoSpikes.cpp'.

BASiCS 1.5.25 (2019-04-07)

• Minor change in 'muUpdateNoSpikes' (C++ function in 'utils_MCMCNoSpikes.cpp') to avoid WARNINGS in bioc-devel related to integers vs unsigned integers

BASiCS 1.5.24 (2019-04-05)

• Minor edit to the documentation of 'makeExampleBASiCS_Data' (fixed link to 'set.seed' documentation as it led to WARNINGS in Bioc-devel)

BASiCS 1.5.23 (2019-04-02)

• Minor edit to the documentation of 'makeExampleBASiCS_Data' (explain why a fixed seed is no longer used)

BASiCS 1.5.22 (2019-04-02)

• 'HiddenCheckValidCombination', 'HiddenGeneParams' and 'HiddenGeneParams' moved from 'Methods.R' to 'HiddenUtils.R'
• 'sapply' replaced by 'vapply' in 'HiddenCheckValidCombination', 'HiddenThresholdSearchDetectHVL_LVG.R' and 'HiddenThresholdSearchTestDE.R'
• Use of 'set.seed' removed from 'makeExampleBASiCS_Data'
• Unit tests updated accordingly
• Adds missing running examples to Rds in order to pass R CMD BioCheck

BASiCS 1.5.21 (2019-04-01)

• Uses built-in chain in examples for 'BASiCS_diagHist' and 'BASiCS_diagPlot'

BASiCS 1.5.20 (2019-04-01)

• Updated documentation for 'BASiCS_MCMC', 'BASiCS_DetectHVG', 'BASiCS_DetectLVG' and 'BASiCS_VarThresholdSearchHVG_LVG'

BASiCS 1.5.19 (2019-03-31)

• 'stats4' added to imports in order to import 'plot' S4 generic.
• 'KernSmooth' removed from DESCRIPTION.
• Maintainer field removed from DESCRIPTION (use Author@R only)
• Updates to travis integration to include BiocCheck

BASiCS 1.5.17 (2019-03-30)

• Minor changes in dependencies to pass R CMD check
• Minor typo fix in documentation of 'newBASiCS_Data'
• '@export' call added to all methods

BASiCS 1.5.16 (2019-03-30)

• 'SingleCellExperiment' moved to depends (DESCRIPTION)
• Explicit calls to external packages (e.g. 'SingleCellExperiment::')
• Unit tests for 'BASiCS_diagHist' and 'BASiCS_diagPlot'
• 'BASiCS_diagHist', 'BASiCS_diagPlot' and 'BASiCS_showFit' moved from methods to functions
• Internal functions marked as 'Hidden'
• 'BASiCS_diagHist', etc moved into separate .R files

BASiCS 1.5.15 (2019-03-27)

• Extended message to suggest additional QC when MCMC sampler fails

BASiCS 1.5.14 (2019-03-27)

• Brackets removed from 'setGeneric' call (as per Hadley Wickham recommendation)
• Removes full import of 'ggplot2' in 'BASiCS_Package.R'
• 'BASiCS_Package.R' is now in alphabetical order

BASiCS 1.5.13 (2019-03-27)

• 'BASiCS_D_TestDE' from deprecated to defunct (follows BioC guidelines)

BASiCS 1.5.12 (2019-03-26)

• R (>= 3.6) is now a requirement

BASiCS 1.5.11 (2019-03-26)

• Edits in BASiCS_Package.R so that 'roxygen2' creates 'NAMESPACE'
• 'testthat' moved from Imports to Suggests

BASiCS 1.5.10 (2019-03-26)

• Corrected ordering in TestDE outpout so that genenames always match
• Small fixes for R CMD check
• Ordering in 'BASiCS_DetectHVG' and 'BASiCS_DetectLVG' can only be done on GeneNames, GeneIndex and Prob

BASiCS 1.5.9 (2019-03-24)

• Alan O'Callaghan is now author
• 'diagPlot' and 'diagHist' methods added to facilitate diagnosis of convergence and mixing for MCMC chains
• Added explicit calls to 'ggplot2' in plot methods.
• 'BASiCS_DetectHVG' and 'BASiCS_DetectLVG' edited based on the "regression" approach (i.e. using epsilon to detect HVGs/LVGs).
• In 'BASiCS_DetectHVG' and 'BASiCS_DetectLVG', options for 'OrderVariable' were simplified (only original order and based on probability)
• Temporary changes in no-spikes version have been restored

BASiCS 1.5.8 (2019-03-22)

• Changes DESCRIPTION to have a single maintainer
• Density plot added to plot Method for BASiCS_Chain objects
• Output plots for plot Method for BASiCS_Chain objects

BASiCS 1.5.7 (2019-03-22)

• Added default value for 'BatchInfo' within 'BASiCS_MCMC'

BASiCS 1.5.6

• Bug fix when not providing BatchInfo as factor
• Extra check if batch names contain spaces
• Added line breaks after individual error messages
• Bug fix that corrects for the number of factors in BatchInfo vector
• Small bug fix in 'test_mcmc_arguments.R'

BASiCS 1.5.5 (2019-03-14)

• Updated vignette to include recommended settings earlier.

BASiCS 1.5.4 (2019-02-12)

• Replaces 'HPDinterval' by 'coda::HPDinterval' in 'BASiCS_showFit' method
• Same as above when calling 'mcmc'
• Changes 'BASiCS_showFit' such that fit line is on top of the dots
• Additional optional arguments ('markExcludedGenes', 'colour', 'GenesSel' and 'colourGenesSel') added to 'BASiCS_showFit' for more flexibility

BASiCS 1.5.3 (2018-12-06)

• Removes '...' argument from 'BASiCS_VarianceDecomp'
• Adds missing argument ('beside') to documentation of 'BASiCS_VarianceDecomp'

BASiCS 1.5.2 (2018-12-01)

• Fixes use of 'BatchInfo' when it cannot be parsed to numeric
• Refactors the use of '...' argument (several functions)

BASiCS 1.5.1 (2018-11-29)

• 'ImmunoOncology' added in biocViews as requested by BioC core team

BASiCS 1.3.24 (2018-10-21)

• Version bump to trigger new build

BASiCS 1.3.23 (2018-10-18)

• Updated vignette to include simple SCE example without spike-in information

BASiCS 1.3.22 (2018-10-19)

• Update of DESCRIPTION to require C++11
• Once again, replacement of 'R::lgammafn' by 'std::lgamma' in c++ code

BASiCS 1.3.21 (2018-10-19)

• Restores use of 'R::lgammafn' due to errors in Bioconductor build report

BASiCS 1.3.20 (2018-10-18)

• Minor updates to README and vignette (e.g. to include BASiCS sticker)

BASiCS 1.3.19 (2018-10-18)

• Replacement of 'R::lgammafn' by 'std::lgamma' in c++ code (great speed-up! with thanks to Shian Su (@Shians))

BASiCS 1.3.18 (2018-10-15)

• 'BASiCS_D_TestDE' has been deprecated (replaced by 'BASiCS_TestDE')
• 'SingleCellExperiment::' added to all calls of 'isSpike'
• Extra input check in 'BASiCS_MCMC' to avoid issues due to multiple types of spike-ins being present in the data.

BASiCS 1.3.17 (2018-10-11)

• New unit tests for different argument settings for the BASiCS_MCMC function

BASiCS 1.3.16 (2018-10-08)

• Reduce checks for Data that was not generated with the newBASiCS_Data function

BASiCS 1.3.15 (2018-10-07)

• Fixed bug when storing chains in the non-spikes case

BASiCS 1.3.13 (2018-09-30)

• Some Rd files generated again

BASiCS 1.3.11 (2018-09-30)

• Alan added as contributor

BASiCS 1.3.10 (2018-09-28)

• Prevent BASiCS_Chain from crashing when StoreAdapt=TRUE for the regression case
• Prevent plot function errors
• Updated documentation using roxygen2

BASiCS 1.3.9 (2018-09-27)

• Changed raw data accessor to 'counts' instead of 'assay'
• makeExampleBASiCS_Data now generates 30 cells instead of 20
• Updated unit tests to match these 30 cells

BASiCS 1.3.8 (2018-09-05)

• Updated README.md (Travis/codecov badges) + updated citation to Cell Systems

BASiCS 1.3.7 (2018-09-05)

• Commit to activate Travis/codecov

BASiCS 1.3.6 (2018-09-04)

• Updated CITATION file

BASiCS 1.3.5 (2018-08-31)

• Updated reference to latest paper

BASiCS 1.3.3 (2018-05-21)

• Missing line added to test_data_examples.R

BASiCS 1.3.2 (2018-05-21)

• Version bump only

BASiCS 1.3.1 (2018-05-21)

• Unit tests created for selected C++ functions ('Hidden_rDirichlet' and 'Hidden_muUpdate')
• Updated unit tests in spike-in parameter estimation to have tolerance (TEMPORARY FIX)
• Minor updates in 'makeExampleBASiCS_Data' and 'newBASiCS_Data' function to allow different spike-in types (as in 'SingleCellExperiment')

BASiCS 1.1.63 (2018-04-27)

• Extra warning message added when 'scran' normalisation fails to produce positive size factors

BASiCS 1.1.62 (2018-04-21)

• 'Regression' is now a compulsory parameter in 'BASiCS_MCMC', hidden functions, documentation and unit tests updated accordingly.
• Minor updates in vignette to clarify default parameter in 'newBASiCS_Data'
• 'BASiCS_Filter' adapted to no-spikes case and minor bug resolved
• Added unit test for 'BASiCS_Filter'
• Minor bug fixed for no-spikes case in 'BASiCS_DenoisedCounts'

BASiCS 1.1.61

• 'Regression' is now a compulsory parameter in 'BASiCS_MCMC', hidden functions and SOME unit tests updated accordingly.

BASiCS 1.1.60 (2018-04-19)

• Updated DESCRIPTION file to introduce residual over-dispersion testing

BASiCS 1.1.59 (2018-04-19)

• Documentation of 'RefFreq' in 'BASiCS_Chain' class.

BASiCS 1.1.58 (2018-04-19)

• Updates in vignette to fully incorporate the regression and non-spike BASiCS models.

BASiCS 1.1.57 (2018-04-16)

• Minor changes in NEWS file

BASiCS 1.1.56 (2018-04-16)

• Minor changes in 'BASiCS_MCMCcppNoSpikes.cpp' to avoid warnings in BioC

BASiCS 1.1.55 (2018-04-16)

• Speed-up of 'BASiCS_TestDE' by avoiding unnecessary calculations

BASiCS 1.1.54 (2018-04-15)

• CITATION file updated to include latest BASiCS bioRxiv preprint

BASiCS 1.1.53 (2018-04-13)

• Fixed bug in plotting for TestDE function
• Added extra code in vignette to construct BASiCS_Data with no spikes
• Added plots to show changes in residual variability during testing

BASiCS 1.1.52 (2018-04-09)

• Added extra sentence to vignette describing the BASiCS_Data generation when SpikeInfo is not available

BASiCS 1.1.51 (2018-03-26)

• Adjusted BASiCS_TestDE function to output data.frames containing same genes.

BASiCS 1.1.50 (2018-03-26)

• Removed OffSet correction for phi in the BASiCS_TestDE function

BASiCS 1.1.49 (2018-03-22)

• Fixed link to 'BASiCS_Chain' documentation in 'BASiCS_showFit' doc

BASiCS 1.1.48 (2018-03-22)

• Excluded epsilon object and RefFreq object from validity test in Chain Class

BASiCS 1.1.47 (2018-03-21)

• Reduced number of genes in data examples
• Unit test updated accordingly
• Nils added as maintainer in DESCRIPTION

BASiCS 1.1.46 (2018-03-21)

• Split C++ code into individual functions
• One file per main function and individual files for utility function
• Created header files for main functions and utility functions

BASiCS 1.1.45 (2018-03-21)

• Messages within C++ code moved to functions

BASiCS 1.1.44 (2018-03-21)

• 'HiddenVarDecomp' adapted to no-spikes case
• Unit test for 'BASiCS_VarDecomp' expanded accordingly
• Specification of 'colnames' and 'rownames' added to 'newBASiCS_Data'
• 'colnames' and 'rownames' are now specified as part of the output of 'BASiCS_DenoisedCounts' and 'BASiCS_DenoisedRates'

BASiCS 1.1.43 (2018-03-20)

• Batch information moved to 'colData' instead of 'metadata' when building a 'SingleCellExperiment' object via the 'newBASiCS_Data' function. This facilitates data subsetting.
• 'BASiCS_MCMC' and 'HiddenBASiCS_MCMC_InputCheck' updated accordingly
• 'SummarizedExperiment::colData' and 'S4Vectors::DataFrame' added as imports in NAMESPACE

BASiCS 1.1.42 (2018-03-20)

• 'OrderVariable' default value set as "GeneIndex" in 'BASiCS_TestDE'
• Fixed usage of 'OrderVariable' in 'BASiCS_TestDE' regression case
• Associated unit test updated accordingly
• Missing denoised rates/counts check added to unit tests for no-spikes case
• CITATION file has been added

BASiCS 1.1.41 (2018-03-20)

• 'BASiCS_MCMC': Default value for 'WithSpikes' set as FALSE when there are no spike-ins in available in the data

BASiCS 1.1.40 (2018-03-20)

• Fixes small bug in 'BASiCS_DenoisedRates', no-spikes case
• Adds denoised rates/counts check to unit tests for no-spikes case

BASiCS 1.1.39 (2018-03-20)

• Denoised counts/rates added to unit test for regression case
• 'BASiCS_DenoisedCounts' adapted for no-spikes case
• 'BASiCS_DenoisedRates' adapted for no-spikes case

BASiCS 1.1.38 (2018-03-20)

• Validity checks updated for 'BASiCS_Chain' and 'BASiCS_Summary' classes. This accounts for different parameter configurations
• 'Summary' method to exclude 'RefFreq' for the no-spikes case
• Unit tests fo no-spikes case updated accordingly

BASiCS 1.1.37 (2018-03-20)

• 'phi' removed from the output of 'BASiCS_MCMC' for no-spikes case
• Unit tests updated accordingly
• Checks for parameter names added to unit tests

BASiCS 1.1.36 (2018-03-18)

• Fixed bug in 'newBASiCS_Data' to define a default value for 'Tech' when spike-ins are not available. Thanks to Muad Abd El Hay (@Cumol) for pointing out this issue.

BASiCS 1.1.35 (2018-03-18)

• New unit tests (more modular): example data, starting values MCMC, MCMC sampler for fixed starting values (spikes/no-spikes; regression/no-regression)

BASiCS 1.1.34 (2018-01-31)

• 'HiddenBASiCS_MCMC_Start' edited to account for new default parameter values in 'scran::computeSumFactors' call
• Unit tests updated accordingly
• Imports/Suggests packages are now in alphabetic order
• Minor style changes suggested by BiocCheck

BASiCS 1.1.33 (2018-01-30)

• In 'HiddenBASiCS_MCMC_Start', 'positive = TRUE' added to 'scran::computeSumFactors' when estimated size factor contain invalid values. Thanks to Mike Morgan for suggesting this solution.

BASiCS 1.1.32 (2018-01-29)

• Fix to ensure that 'BASiCS_MCMC' function adds cell labels for $\phi$
• 'makeExampleBASiCS_Data' now produces valid 'colnames' (cell labels)
• Fixed colnames of $\phi$ parameter in all data examples
• Extended validity test for 'BASiCS_Chain' class
• 'rownames' and 'colnames' methods created for 'BASiCS_Chain' class
• Added example and unit test for 'BASiCS_VarianceDecomp' function

BASiCS 1.1.31 (2018-01-22)

• Updated documentation for 'BASiCS_showFit' method

BASiCS 1.1.30 (2018-01-22)

• Commit to triger a new built

BASiCS 1.1.29 (2017-12-21)

• 'showFit' generic renamed as 'BASiCS_showFit' (to avoids potential conflicts)

BASiCS 1.1.28 (2017-12-20)

• Vignette header as in BiocStyle
• In 'BASiCS_TestDE' function: 'ProbThresholdE' argument renamed as 'ProbThresholdR'
• In 'BASiCS_TestDE' function: 'ProbThresholdE' argument renamed as 'ProbThresholdR'
• Updated documentation for example 'BASiCS_Chain' objects
• Minor additional changes to the documentation

BASiCS 1.1.27 (2017-12-20)

• Minor typo resolved in 'displayChainBASiCS' method
• Reduced size of example objects
• Unit tests updated accordingly
• In 'BASiCS_TestDE' function: 'PsiE' argument renamed as 'EpsilonR'

BASiCS 1.1.26 (2017-12-20)

• Vignette bibliography moved to .bib file
• Added diagram to summarise different implementations
• Reduced size of example objects
• Unit tests updated accordingly
• 'subset' method created for 'BASiCS_Chain' objects
• Removal of parameter 'lambda' from 'BASiCS_Chain' objects (for storage)
• R/Methods.R + R/Classes.R updated accordingly
• 'newBASiCS_Chain' updated accordingly.
• Code format for 'showFit'

BASiCS 1.1.24 (2017-12-18)

• Reduced no of iterations in unit test for quicker testing
• library 'hexbin' added to imports (required for 'showFit')
• Vignette edits (simplification of Quick Start)

BASiCS 1.1.23 (2017-12-18)

• Minor improvements to documentation

BASiCS 1.1.22 (2017-12-15)

• Documentation on ChainSCReg and ChainRNAReg datasets added
• Fixed showFit method
• Updated dpi option in vignette to reduce .html size
• Default value for 'ConstrainProp' set to 0.20 (no-spikes)
• Unit tests updated accordingly (no-spikes)

BASiCS 1.1.21 (2017-12-13)

• 'ConstrainProp' added as an optional argument for 'BASiCS_MCMC' (no-spikes)

BASiCS 1.1.20 (2017-12-11)

• Updated dpi option in vignette

BASiCS 1.1.19 (2017-12-09)

• extended vignette to describe regression and non-spike case
• changed markdown to rmarkdown engine to compile vignette to include table of contents

BASiCS 1.1.18 (2017-12-08)

• Minor typo in 'HiddenBASiCS_MCMC_NoSpikesParam' resolved

BASiCS 1.1.17 (2017-12-07)

• Stop scaling of size factors for no-spikes case ('HiddenBASiCS_MCMC_Start')
• Unit testing updated accordingly
• Extra unit test to ensure that no-spikes results match for objects with/without spikes when setting 'WithSpikes = FALSE'
• Modified constrain for no-spikes cases (to deal with non-zero genes)
• Default value of 'ConstrainType' set to 1 in 'BASiCS_MCMC' (no-spikes only)

BASiCS 1.1.16 (2017-11-29)

• Change in 'BASiCS_MCMC' no-spikes so that only genes with zero total counts are excluded from the identifiability constrain

BASiCS 1.1.15 (2017-11-29)

• Typo fixed in 'AtLeast2Cells' ('BASiCS_MCMC' function) definition for no-spikes + regression case when original data has spikes

BASiCS 1.1.14 (2017-11-29)

• Minor bug resolved for no-spikes case when original data has spikes
• New unit test to assess that case

BASiCS 1.1.13 (2017-11-28)

• Fixed storage of 'RefGene' in no-spikes when 'StochasticRef = FALSE'

BASiCS 1.1.12 (2017-11-28)

• Additional changes to improve usage of no-spikes case

BASiCS 1.1.11 (2017-11-24)

• Minor typo in the call to 'HiddenBASiCS_MCMCcppNoSpikes' has been resolved

BASiCS 1.1.10 (2017-11-27)

• 'HiddenBASiCS_MCMC_Start' updated to remove regression-related hyper-params
• 'HiddenBASiCS_MCMC_ExtraArgs' updated to include regression-related hyper-par
• 'BASiCS_MCMC' modified accordingly
• Storage of adaptive variances fixed for the no-spike case

BASiCS 1.1.9 (2017-11-24)

• 'means' only updated when needed (regression case); unit test updated accordingly
• 'deltaUpdateNoSpikes' + 'deltaUpdateRegNoSpikes' removed as no longer required
• Simplification of terms in 'deltaUpdateReg'
• Small changes to unify code format in C++ file
• Notation change: 'phi' replaced by 's' in no-spikes implementation
• Unit test changed accordingly (no-spike)
• Minor style changes in 'BASiCS_MCMC'
• 'BASiCS_MCMC' function broken into smaller functions (easier to read). This creates the following hidden functions: 'HiddenBASiCS_MCMC_InputCheck', 'HiddenBASiCS_MCMC_ExtraArgs', 'HiddenBASiCS_MCMC_NoSpikesParams', 'HiddenBASiCS_MCMC_OutputStore' and 'HiddenBASiCS_MCMC_RefFreqStore'
• Merge between no-spikes and regression case completed (code to be tested)
• Minor change in storage of reference frequency (no spikes only)

BASiCS 1.1.8 (2017-11-21)

• 'muUpdateRegNoSpikes' and 'deltaUpdateRegNoSpikes' added to C++ code
• Clean-up of C++ code (repeated debug checks made into function)
• 'lambdaUpdateReg' created as a separate function
• Vectorization of calculations related to regression implementation
• Global quantities (e.g. inv(V0)) taken outside the look (regression case)
• 'sigma2UpdateReg' created as a separate function
• 'betaUpdateReg' created as a separate function
• Fixed typo in sigma2 updates (regression case); unit test updated accordingly

BASiCS 1.1.7 (2017-11-20)

• Nils added as author in cpp file
• Updated unit test for no-spikes case (changes due to change in stoch ref)
• Change in 'BASiCS_MCMC' so that only biological counts go to C++
• Added factorizations in 'muUpdateReg' and 'deltaUpdateReg' (C++ code)

BASiCS 1.1.6 (2017-11-15)

• Added prototype for regression + no-spikes sampler

BASiCS 1.1.5 (2017-11-15)

• Removal of collapsed sampler prototype (from C++ and R) - moved to 'CollapsedSampler' branch
• Number of genes used for stochastic reference increased to 10% of genes (no spikes only)

BASiCS 1.1.4 (2017-11-12)

• Only include genes that are expressed in at least 2 cells per condition for differential residual dispersion testing (regression case only)

BASiCS 1.1.3 (2017-11-08)

• Collapsed sampler implemented (to be tested)
• Unit tests reverted to original case
• Version number bump
• Store 'TableRef' on the 'StoreDir' directory (no-spike case only)

BASiCS 1.1.2 (2017-11-08)

• Skeleton for sampler with integrated out s

BASiCS 1.1.1 (2017-11-08)

• 'ggplot2' added to imports
• Default value for SpikeInfo changed to NULL in 'newBASiCS_Data' function
• Cleaning of 'HiddenBASiCS_MCMCcppNoSpikes'
• Cleaning of full conditionals for no-spikes implementation
• Fixed bug in stochastic reference implementation
• Added unit test for no-spikes case (estimation)
• Minor tyle changes to merge regression case
• 'Eta' parameter removed from 'Summary' method (regression case only)
• Corrected HPD interval calculation for epsilon and sigma2 (regression case)
• Added mark for 'ExcludedFromRegression' genes in 'BASiCS_TestDE'

BASiCS 1.1.0 (2017-08-16)

• Minor changes required to pass BiocCheck (used formatR and BiocChecks)
• Version number bump after bioconductor 3.6 release

BASiCS 1.0.13 (2017-08-15)

• Minor changes to documentation
• Minor changes to vignette

BASiCS 1.0.12 (2017-08-14)

• 'SummarizedExperiment' class replaced by 'SingleCellExperiment'
• Updated vignette

BASiCS 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
• 'WithSpikes' argument removed from 'BASiCS_LoadChain' function

BASiCS 1.0.10 (2017-08-06)

• BASiCS_TestDE : changes in output messages
• Gene name added in plot method for BASiCS_Chain objects

BASiCS 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

BASiCS 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

BASiCS 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

BASiCS 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)

BASiCS 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

BASiCS 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)

BASiCS 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

BASiCS 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

BASiCS 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)

BASiCS 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
• Bioconductor 3.6 release

BASiCS 0.99.14 (2017-10-19)

• Added checks to ensure input 'SingleCellExperiment' object has all info

BASiCS 0.99.13 (2017-10-17)

• @neling email added to DESCRIPTION + author contributions

BASiCS 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

BASiCS 0.99.10 (2017-10-17)

• Updated README with BioC installation instructions and @nturaga acknowledgment

BASiCS 0.99.9 (2017-10-16)

• Updated URL and BugReports in DESCRIPTION

BASiCS 0.99.8 (2017-10-10)

• version bump to trigger a new Bioconductor build

BASiCS 0.99.7

• 'inst' folder has been deleted
• Removal of '...' arg in 'segments' - 'plot' method for 'BASiCS_Summary'

BASiCS 0.99.5 (2017-09-26)

• Change of default 'PriorDelta' value in 'BASiCS_MCMC'
• Unit tests modified accordingly

BASiCS 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

BASiCS 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
• 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'
• Removal of second example in 'makeExampleBASiCS_Data' (no longer required due to DataSC, DataRNA)
• Format for 'makeExampleBASiCS_Data'
• Format for 'BASiCS_Sim'
• 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'
• Calculations in 'BASiCS_DenoisedRates' moved to C++ to increase speed
• 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
• Edits in 'HiddenBASiCS_MCMCcpp' and associated C++ functions * Optimization of MH updates
• Edits in 'HiddenBASiCS_MCMCcpp' and associated C++ functions * Batch & no-batch versions merged in a single function * Avoids double transponse for chain storage

BASiCS 0.99.2

• 'newBASiCS_Data': format + checks moved to 'HiddenChecksBASiCS_Data' function
• 'HiddenChecksBASiCS_Data': use of colMeans2, rowMeans2
• Format in welcome message
• 'newBASiCS_Chain': format

BASiCS 0.99.0 (2017-08-28)

• Minor changes to complete Bioconductor submission checklist
• Version re-numbered according to Bioconductor guidelines

BASiCS 0.7.30 (2017-07-26)

• Typo fixed in 'BASiCS:::HiddenBASiCS_MCMC_Start' function (thanks to @bdulken for pointing out this issue)

BASiCS 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)

BASiCS 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.

BASiCS 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.

BASiCS 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)

BASiCS 0.7.25 (2017-01-11)

• Fixed typo in vignette file (thanks to Dmitriy Zhukov for pointing this out)

BASiCS 0.7.24 (2016-11-23)

• Median changed to mean when calculating identifiability constrain for the no spike case

BASiCS 0.7.23 (2016-11-21)

• Cleaning-up of identifiability constrain options for the no spike case

BASiCS 0.7.22 (2016-11-16)

• Fixed bug for 'ConstrainType' = 5 (affects no spike case only)

BASiCS 0.7.21 (2016-11-15)

• 'ConstrainType' = 4, 5 added (exclude genes with capture in less than 'ConstrainLimit'100% of the cells)

BASiCS 0.7.20 (2016-11-14)

• 'newBASiCS_Data' function modified to allow no spikes case

BASiCS 0.7.19 (2016-11-14)

• RefGene information to be stored as .txt file

BASiCS 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

BASiCS 0.7.17 (2016-11-07)

• Error fixed in the definition of RefGenes

BASiCS 0.7.16 (2016-11-07)

• ConstrainType = 3 (stochastic ref) re-introduced for no-spikes case

BASiCS 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

BASiCS 0.7.14 (2016-11-03)

• Debug message removed from 'muUpdateNoSpikes' function.

BASiCS 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!

BASiCS 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

BASiCS 0.7.11 (2016-10-31)

• Comments added to clarify no spikes case in 'BASiCS_MCMC' function.

BASiCS 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

BASiCS 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

BASiCS 0.7.8 (2016-08-15)

• ConstrainType = 4 implemented (no spikes case only)

BASiCS 0.7.7 (2016-08-12)

• ConstrainType = 3 implemented (no spikes case only)

BASiCS 0.7.6 (2016-08-11)

• As v 0.7.5 but with extra argument for constrain limit (no spikes case only)

BASiCS 0.7.5 (2016-08-10)

• Modified constrain to include 'expressed' genes only (no spikes case only)

BASiCS 0.7.4 (2016-08-09)

• Modified constrain to include 'expressed' genes only (no spikes case only)

BASiCS 0.7.3 (2016-08-08)

• Reference set to be the gene closest to the average (no spikes case only)

BASiCS 0.7.2 (2016-08-05)

• Same as v 0.7.2 but more efficient

BASiCS 0.7.1 (2016-08-05)

• Random reference in sequential updates for mu (no spikes case only)

BASiCS 0.7.0 (2016-08-02)

• Sequential updates for mu in MCMC (no spikes case only)

BASiCS 0.6.9 (2016-08-01)

• Dirichlet-based proposals for mu in MCMC (no spikes case only)

BASiCS 0.6.8 (2016-07-28)

• Sequential updates for mu in MCMC (no spikes case only)

BASiCS 0.6.7 (2016-07-28)

• Minor changes in the validity checks of 'BASiCS_D_Data' objects

BASiCS 0.6.6 (2016-07-27)

• First working version of no spikes case (constrained mu's)

BASiCS 0.6.5

• Modified identifiability constrains for no spikes case.

BASiCS 0.6.4 (2016-06-01)

• Safety checks added to 'phiUpdateNoSpikes'

BASiCS 0.6.3 (2016-05-31)

• Small update in wellcome message.

BASiCS 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)

BASiCS 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

BASiCS 0.5.11 (2016-05-24)

• 'importMethodsFrom(scran, computeSumFactors)' added to NAMESPACE

BASiCS 0.5.10 (2016-05-20)

• Updated bug in 'HiddenBASiCS_MCMC_Start' function (thanks to Joanna Dreux for noticing this issue)

BASiCS 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

BASiCS 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

BASiCS 0.5.7 (2016-04-27)

• Welcome message added

BASiCS 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.

BASiCS 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.

BASiCS 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.

BASiCS 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).

BASiCS 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.

BASiCS 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)

BASiCS 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

BASiCS 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.

BASiCS 0.4.0 (2015-12-21)

• Preliminary functions for differential expression analyses (mean and over-dispersion) have been added.

BASiCS 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.

BASiCS 0.3.4 (2015-11-11)

• Fix of example code of 'newBASiCS_Data' function. Thanks to Simon Andrews for pointing out this issue.

BASiCS 0.3.3 (2015-11-05)

• Same method as before but improved performance of C++ code

BASiCS 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.

BASiCS 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

BASiCS 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)

BASiCS 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.

BASiCS 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

BASiCS 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

BASiCS 0.1.5 (2015-05-27)

• Small typo in 'BASiCS_VarThresholdSearchHVG' and 'BASiCS_VarThresholdSearchLVG' has been fixed.

BASiCS 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).

BASiCS 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.

BASiCS 0.1.2 (2015-04-23)

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

BASiCS 0.1.1 (2015-04-21)

• Improved documentation

BASiCS 0.1 (2015-04-20)

• Original release