NEWS

                        Changes in version 1.19.1
                        
+ added J Gilis, D Risso, L Clement as authors
+ differential detection with 'pbDS(..., method="DD")' or 'pbDD()'
  & stagewise testing [Gilis et al.], plus corresponding vignette
+ replace 'aes_string()' in 'ggplot()' by '.data$.' from 'rlang'
  
                        Changes in version 1.15.1
                        
+ 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.
  
+ bug fix in 'mmDS': 'dream' (new version?) wouldn't recognize
  model variables provided as data; fixed via adding 'as.formula()'.
  
+ "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
                        
+ Bioconductor release v3.17

                        Changes in version 1.12.1

+ fixed various typos in both vignettes
+ internal fixes to keep up with 'ggplot2' & 'dplyr' updates
+ bug fix in 'simDS' computing means when one group is missing
+ bug fix in 'resDS' until testing when 'cpm/frq = TRUE'

                        Changes in version 1.11.1

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

                        Changes in version 1.9.3

+ 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

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

+ 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

+ Bioconductor 3.14 release

                        Changes in version 1.7.2

+ 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

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

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

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

+ significant speed-up of aggregateData() by replacing usage  
  of rowX() over a list with scuttle::summarizeAssayByGroup()
  
+ added options use "prop.detected" and "num.detected" 
  as summary statistic (argument 'fun') in aggregateData()

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

+ aggregateData() now stores the number of cells that went into aggregation under
  int_colData(.)$n_cells (vs. metadata(.)$n_cells) to support automated subsetting
  
+ replaced argument n_threads with BPPARAM throughout all 
  parallelizable functions (aggregateData(), pbDS(), mmDS())
  
+ bug fix in prepSim(): the function previously failed when 
  cluster/sample/group_id cell metadata columns were non-factors
  
+ bug fix in resDS(): cpm = TRUE previously didn't handle
  missing cluster-sample combinations correctly