Changes in version 1.27.2                        

    o   added logFC shrinkage option and downstream arguments to 'pbDS'

    o   changed default edgeR normalization from TMM to TMMwsp

                       Changes in version 1.25.4                        

    o   update Gilis et al. citation for DD

    o   remove 'cowplot' in favor of 'patchwork'

    o   move 'IHW', 'DESeq2' and 'sctransform' to 'Suggests:'

    o   omit 'data.table' and 'purrr' everywhere and remove from 'Imports:'

    o   #102 fix: use correct CPM values in 'resDS' when 'method=limma-voom'

                       Changes in version 1.25.3                        

    o   up R version dependency to ≥ 4.6

    o   rename 'edgeR::calcNormFactors' to 'normLibSizes'

                       Changes in version 1.25.2                        

    o   bug fix in '.mm_dream' (underlying 'mmDS' methods 'poisson' and 'nbinom'):
	transform size factors from linear- to log-scale before being used as offset

                       Changes in version 1.25.1                        

    o   fix #146: support for sparse matrices by 'pbDS'

    o   updated Germain et al. citation for BBHW

                       Changes in version 1.24.0                        

    o   Bioconductor 3.22 release

                       Changes in version 1.23.2                        

    o   fixed unit test with edge-case failure

    o   added missing '@importFrom grDevices hcl.colors'

    o   fixed 'BiocParallel::SerialParam progressbar' arg

                       Changes in version 1.23.1                        

    o   added bulk-based hypothesis weighing

                       Changes in version 1.23.0                        

    o   Bioconductor 3.21 release

                       Changes in version 1.19.1                        

    o   added J Gilis, D Risso, L Clement as authors

    o   differential detection with 'pbDS(..., method="DD")' or 'pbDD()'
	& stagewise testing [Gilis et al.], plus corresponding vignette

    o   replace 'aes_string()' in 'ggplot()' by '.data$.' from 'rlang'

                       Changes in version 1.15.1                        

    o   bug fix in 'pbDS': too stringent filtering causing no genes in any clusters
	to be tested previously resulted in a 'subscript out of bounds' error;
	execution is stopped and an informative error thrown instead.

    o   bug fix in 'mmDS': 'dream' (new version?) wouldn't recognize
	model variables provided as data; fixed via adding 'as.formula()'.

    o   "analysis" vignette: replaced suspended 'dplyr' function
	'top_n' with 'slice_min' when filtering for top DS hits;
	fixed some typos; updated preprint to journal reference.

                       Changes in version 1.15.0                        

    o   Bioconductor release v3.17

                       Changes in version 1.12.1                        

    o   fixed various typos in both vignettes

    o   internal fixes to keep up with 'ggplot2' & 'dplyr' updates

    o   bug fix in 'simDS' computing means when one group is missing

    o   bug fix in 'resDS' until testing when 'cpm/frq = TRUE'

                       Changes in version 1.11.1                        

    o   bug fix in pbHeatmap(): previously failed for results from 'mmDS()'

                        Changes in version 1.9.3                        

    o   bug fix in pbDS(): drop samples w/o any detected features,
	otherwise edgeR::calcNormFactors() fails when lib.size 0

                        Changes in version 1.8.1                        

    o   bug fix in prepSim(): removal of genes with NA coefficients
	was previously not propagated to the dispersion estimates 

    o   bug fix in test-resDR.R: set 'min_cells = 0' to assure that
	everything is being tested, otherwise unit tests could fail

                        Changes in version 1.8.0                        

    o   Bioconductor 3.14 release

                        Changes in version 1.7.2                        

    o   bug fix in prepSim(): removal of NA coefficients and 
	subsetting of the input SCE was previously out of synch

                        Changes in version 1.5.2                        

    o   added edgeR::calcNormFactors() step in prepSim()

    o   added argument 'dd' to simData() specifying  
	whether or not to simulate 2 groups

    o   prepSim() and simData() now support simulation of "singular" design  
	(no samples, no clusters), as well as only samples/clusters

    o   simData() defaults to simulating as many samples as available  
	in order to avoid re-use (duplication) of reference samples

                        Changes in version 1.5.1                        

    o   significant speed-up of aggregateData() by replacing usage  
	of rowX() over a list with scuttle::summarizeAssayByGroup()

    o   added options use "prop.detected" and "num.detected" 
	as summary statistic (argument 'fun') in aggregateData()

    o   added parallelization support in aggregateData() and pbDS() through argument BBPARAM
	(passed to scater::sumCountsAcrossCells() and BiocParallel::bplapply, respectively)

    o   aggregateData() now stores the number of cells that went into aggregation under
	int_colData(.)$n_cells (vs. metadata(.)$n_cells) to support automated subsetting

    o   replaced argument n_threads with BPPARAM throughout all 
	parallelizable functions (aggregateData(), pbDS(), mmDS())

    o   bug fix in prepSim(): the function previously failed when 
	cluster/sample/group_id cell metadata columns were non-factors

    o   bug fix in resDS(): cpm = TRUE previously didn't handle
	missing cluster-sample combinations correctly