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Changelog

Source: NEWS.md

dreamlet 1.4.0

  • Nov 5, 2024
  • update to Bioc 3.20

dreamlet 1.3.4

dreamlet 1.3.3

dreamlet 1.3.1

  • May 31, 2024
  • bump Bioc version

dreamlet 1.1.24

dreamlet 1.1.23

  • May 16, 2024
  • processOneAssay, set rescaleWeightsAfter=FALSE by default

dreamlet 1.1.22

  • May 14, 2024
  • fix issue in topTable() with multiple coef values

dreamlet 1.1.21

dreamlet 1.1.20

  • in dreamlet() allow formula to include only intercept

dreamlet 1.1.19

dreamlet 1.1.18

  • bug fix

dreamlet 1.1.17

  • new functionality in plotPCA() and outlierByAssay()
  • works on any list, not just dreamletProcessedData
  • allows outlier analysis on residuals

dreamlet 1.1.16

dreamlet 1.1.15

  • Feb 5, 2024
  • Fix bug in call to eBayes()
  • in processAssays() pass argument scaledByLib to voomWithDreamWeights()

dreamlet 1.1.14

  • Jan 29, 2024
  • fix bug in pbWeights()
  • smaller pseudo variance
  • limit to only expressed genes by adding getExprGeneNames()

dreamlet 1.1.13

dreamlet 1.1.12

dreamlet 1.1.11

dreamlet 1.1.10

dreamlet 1.1.9

  • Jan 3, 2024
  • use get_metadata_aggr_means() to extract aggr_means when SCE is produced by cbind’ing

dreamlet 1.1.8

  • Dec 18, 2023
  • fix issue when no genes pass cutoffs
  • fix issue with aggr_means in aggregateToPseudoBulk()
  • fix bug when rdf is low for all genes

dreamlet 1.1.7

dreamlet 1.1.6

  • Dec 5, 2023
  • pbWeights() add argument maxRatio

dreamlet 1.1.5

  • Nov 28, 2023
  • fix edge cases in pbWeights()
  • cell weights is not default in dreamlet()

dreamlet 1.1.4

  • Nov 27, 2023
  • add pbWeights() to compute precision weights for pseudobulk counts
  • extend extractData() and include it in vignette

dreamlet 1.1.3

  • Nov 22, 2023
  • add stackAssays()
  • add diffVar()
  • fix getVarFromCounts) so zeta is a mean, not a sum

dreamlet 1.1.2

dreamlet 1.0.1 / 1.1.1

  • bug fix in Bioc 3.18 and devel

dreamlet 0.99.33

dreamlet 0.99.32

  • Oct 18, 2023
  • update variancePartition version dependency
  • add getWeightsList()

dreamlet 0.99.31

dreamlet 0.99.30

  • Sept 22, 2023
  • Fix issue with precision weights from cell number
  • Include setAutoBlockSize() update within aggregateToPseudoBulk()

dreamlet 0.99.28

dreamlet 0.99.26

  • August 18, 2023
  • Update error handling and documentation

dreamlet 0.99.23

  • August 8, 2023
  • run styler::style_pkg()

dreamlet 0.99.22

dreamlet 0.99.21

dreamlet 0.99.20

  • June 29, 2023
  • in processAssays() use voomWithDreamWeights(..., span="auto") to estimate the lowess tuning parameter
  • rare error in merge_metadata() when a cell type is not observed for all donors.

dreamlet 0.99.19

  • June 28, 2023
  • in dreamlet() fix issue when contrasts are specified and formula includes variable from metadata()

dreamlet 0.99.18

dreamlet 0.99.14

dreamlet 0.99.13

  • May 31, 2023
  • improved error reporting
  • Compatibility with variancePartition v2.0.5 (renamed 1.31.1)

dreamlet 0.99.12

dreamlet 0.99.11

  • May 12, 2023
  • Compatibility with variancePartition v2.0.1

dreamlet 0.99.10

dreamlet 0.99.6

  • March 29, 2023
  • fix topTable() for dreamletResult in the case where one or more cells didn’t estimate the coefficient of interest

dreamlet 0.99.3

dreamlet 0.99.1

dreamlet 0.99.0

  • March 15, 2023
  • Biocondcutor submission

dreamlet 0.0.64

  • March 7, 2023
  • fix topTable() to deal with multiple coef as array
  • add vignette about non-linear effects
  • Add colData<- for dreamletProcessedData

dreamlet 0.0.63

  • March 3, 2023
  • small bug fixes in topTable() and plotForest()

dreamlet 0.0.62

dreamlet 0.0.61

dreamlet 0.0.60

  • Jan 18, 2023
  • allow custom ordering of assays in plots

dreamlet 0.0.59

  • Jan 12, 2023
  • update plotVolcano() to allow scales="free_y"
    • warning when p-values are zero.

dreamlet 0.0.58

dreamlet 0.0.57

dreamlet 0.0.56

dreamlet 0.0.55

dreamlet 0.0.54

dreamlet 0.0.53

  • Nov 18, 2022
  • fix bug in topTable()

dreamlet 0.0.52

dreamlet 0.0.51

dreamlet 0.0.50

  • Nov 2, 2022
  • fix bug in zenith_gsa() for few gene sets

dreamlet 0.0.49

dreamlet 0.0.48

  • Sept 14, 2022
  • add transpose argument to plotGeneHeatmap()
  • and alpha arugment to plotVoom()
  • update y axis and outlines in plotVarPart()

dreamlet 0.0.47

  • update filtering of covariates, especially for when many samples are dropped

dreamlet 0.0.46

dreamlet 0.0.45

  • update documentation

dreamlet 0.0.44

dreamlet 0.0.43

dreamlet 0.0.42

  • fix misc issues with plotting and order of facets
  • fix issue with redundant variables in small sample sizes

dreamlet 0.0.41

  • fix issue with topTable() when all random effects are dropped

dreamlet 0.0.40

  • Compatibility with zenith package submitted to Bioconductor.

dreamlet 0.0.39

dreamlet 0.0.38

dreamlet 0.0.37

dreamlet 0.0.36

dreamlet 0.0.35

  • remove old code and dependencies
  • change website theme

dreamlet 0.0.34

dreamlet 0.0.33

dreamlet 0.0.32

  • add colsum2() using beachmat code.

dreamlet 0.0.31

dreamlet 0.0.30

  • update run_mash() to combine results across coefs

dreamlet 0.0.29

  • fix bug in dreamlet::colsum_fast() used in pseudobulk

dreamlet 0.0.28

  • add da_to_sparseMatrix()

dreamlet 0.0.27

  • aggregateToPseudoBulk() for DelayedArray now uses colsum_fast()
    • this is faster then the previous version for DelayedArray

dreamlet 0.0.26

  • update dreamletCompareClusters():
    • now compatable with plotZenithResults()
    • include flag errorsAsWarnings. If TRUE warns and returns NULL.

dreamlet 0.0.25

dreamlet 0.0.24

dreamlet 0.0.23

dreamlet 0.0.22

dreamlet 0.0.21

dreamlet 0.0.20

dreamlet 0.0.19

dreamlet 0.0.18

dreamlet 0.0.17

dreamlet 0.0.16

dreamlet 0.0.15

  • processOneAssay() weights by number of cells
  • require variancePartition >= 1.25.1 to handle weights in voomWithDreamWeights()
  • fix bug in topTable()
  • add plotPercentBars() for class vpDF
  • misc bug fixes
  • improve documentation

dreamlet 0.0.14

  • move count ratio code to crumblr package
  • use applyQualityWeights()

dreamlet 0.0.13

  • Oct 25, 2021
  • add ilr_composition_test.R

dreamlet 0.0.12

  • Oct 15, 2021
  • update print for dreamletResult using coefNames()
  • small bug fix
  • fix bugs in regModel()

dreamlet 0.0.11

  • Oct 6, 2021
  • removeConstantTerms() now doesn’t drop terms solely because of NA’s
    • this means that other functions can gracefully warn the user about NA’s

dreamlet 0.0.10

  • Oct 5, 2021

  • suppress package startup messages in aggregateToPseudoBulk()

  • bug fix in removeConstantTerms()

  • Sept 30, 2021

  • call to zenith_gsa() adds argument inter.gene.cor and progressbar

  • fix output to cellTypeCompositionVarPart() and cellTypeCompositionTest()

  • fix issue with topTable() where FDR was evaluated on only a subset of genes

dreamlet 0.0.8

  • Sept 28, 2021
  • update docs, logos, TODO
  • update dreamlet() to handle linear contrasts
  • removeConstantTerms() now drops categorical variables with only a max of one example per category
  • Cleaner code for cell composition test

dreamlet 0.0.7

  • Sept 2, 2021
  • add cellTypeCompositionTest()
    • handle random effects

dreamlet 0.0.6

  • Sept 1, 2021
  • enforce package version requirements

dreamlet 0.0.5

  • August 25, 2021
  • handling of pmetadata by processAssays(), fitVarPart(), and dreamlet()
  • change defaults for bpparam to SerialParam()
  • Created new files for code
  • Create object dreamletResult returned by dreamlet() and used by topTable()
  • more capable dreamletProcessedData object
  • add details() functions for dreamletResult, dreamletProcessedData and vpDF
  • More information about when terms are dropped from formulas
  • type definition to zenith_gsa

dreamlet 0.0.4

  • add aggregateToPseudoBulk() for faster access to SingleCellExperiment() backed by H5AD

dreamlet 0.0.3

  • add argument to processAssays() to include extra meta-data
  • add subseting with assay() for dreamletProcessedData
  • adapt plotVoom(), plotVolcano(), plotVarPart() to be more flexiable
  • fitVarPart() returns DataFrame

dreamlet 0.0.2

  • check failed regression

dreamlet 0.0.1

  • Initial version