NEWS

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muscat 1.27.2

• added logFC shrinkage option and downstream arguments to 'pbDS'
• changed default edgeR normalization from TMM to TMMwsp

muscat 1.25.4

• update Gilis et al. citation for DD
• remove 'cowplot' in favor of 'patchwork'
• move 'IHW', 'DESeq2' and 'sctransform' to 'Suggests:'
• omit 'data.table' and 'purrr' everywhere and remove from 'Imports:'
• #102 fix: use correct CPM values in 'resDS' when 'method=limma-voom'

muscat 1.25.3

• up R version dependency to ≥ 4.6
• rename 'edgeR::calcNormFactors' to 'normLibSizes'

muscat 1.25.2

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

muscat 1.25.1

• fix #146: support for sparse matrices by 'pbDS'
• updated Germain et al. citation for BBHW

muscat 1.24.0

• Bioconductor 3.22 release

muscat 1.23.2

• fixed unit test with edge-case failure
• added missing '@importFrom grDevices hcl.colors'
• fixed 'BiocParallel::SerialParam progressbar' arg

muscat 1.23.1

• added bulk-based hypothesis weighing

muscat 1.23.0

• Bioconductor 3.21 release

muscat 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'

muscat 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.

muscat 1.15.0

• Bioconductor release v3.17

muscat 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'

muscat 1.11.1

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

muscat 1.9.3

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

muscat 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

muscat 1.8.0

• Bioconductor 3.14 release

muscat 1.7.2

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

muscat 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

muscat 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