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NEWS.md

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dreamlet 1.4.0

  • Nov 5, 2024
  • update to Bioc 3.20

dreamlet 1.3.4

  • Oct 27, 2024
  • Better error reporting addressing #25

dreamlet 1.3.3

dreamlet 1.3.1

  • May 31, 2024
  • bump Bioc version

dreamlet 1.1.24

  • May 28, 2024
  • dreamlet() gives clearer error message for singular design matrix
  • plotGeneHeatmap() handles zmax correctly now

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

  • fix issue in run_mash() with multiple coefficients

dreamlet 1.1.20

  • in dreamlet() allow formula to include only intercept

dreamlet 1.1.19

  • bug fix in compositePosteriorTest()

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

  • Feb 8, 2024
  • fix bug in pbWeights()
  • Fix scaling issue in outlierByAssay()

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

  • Jan 25, 2024
  • improve error reporting in seeErrors() and documentation
  • update outlier() to compute z-scores. How returns data.frame()
  • add outlierByAssay() and plotPCA()

dreamlet 1.1.12

  • Jan 16, 2024
  • compositePosteriorTest() allows exclude set to be NULL

dreamlet 1.1.11

  • Jan 16, 2024
  • add meta_analysis()

dreamlet 1.1.10

  • Jan 10, 2024
  • stackAssays() now includeds metadata()$aggr_means correctly
  • add compositePosteriorTest()

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

  • Dec 10, 2023
  • add plotBeeswarm()
  • add rowWeightedVarsMatrix()
  • bug fixes
  • add isFullRank() check in dreamlet()
  • handle exceptions in run_mash()

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

  • Nov 13, 2023
  • computeLogCPM() uses augmentPriorCount()

dreamlet 1.0.1 / 1.1.1

  • bug fix in Bioc 3.18 and devel

dreamlet 0.99.33

  • computeLogCPM() now returns matrix instead of sparseMatrix

dreamlet 0.99.32

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

dreamlet 0.99.31

  • Oct 12, 2023
  • fix error reporting in processAssays()

dreamlet 0.99.30

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

dreamlet 0.99.28

  • Sept 5, 2023
  • Update error handling for processAssays() and fitVarPart()

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

  • August 8, 2023
  • dreamletCompareClusters() now allows cell-level covariates in response to #11
  • Fix code for Bioconductor submission

dreamlet 0.99.21

  • July 17, 2023
  • Improve functionality and documentation of dreamlet::residuals()

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

  • June 27, 2023
  • add assays argument to buildClusterTreeFromPB()

dreamlet 0.99.14

  • June 16, 2023
  • bug fix in processAssays() when assays is dropped

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

  • March 23, 2023
  • reduce compiler time
  • add computeNormCounts() and computeLogCPM()

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

  • Feb 27, 2023
  • aggregateToPseudoBulk() stores mean of cell-level covariates in metadata(pb)$aggr_means
  • Use these covariates in processAssays(), dreamlet(), fitVarPart()
  • extend to aggregateNonCountSignal()

dreamlet 0.0.61

  • Jan 25, 2023
  • add plotProjection()
  • add outlier()
  • update plotForest()

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

  • Jan 9, 2023
  • RewriteaggregateNonCountSignal() to include filters
  • Depend only on CRAN and BioC packages

dreamlet 0.0.57

  • Jan 4, 2023
  • Include precision weights in aggregateNonCountSignal()

dreamlet 0.0.56

  • Jan 3, 2023
  • Enable processing of non-count data with aggregateNonCountSignal()

dreamlet 0.0.55

  • Dec 7, 2022
  • in plotGeneHeatmap() drop empty genes

dreamlet 0.0.54

  • Nov 30, 2022
  • add buildClusterTreeFromPB()

dreamlet 0.0.53

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

dreamlet 0.0.52

  • Nov 18, 2022
  • add as.dreamletResult()
  • update variancePartition dependency and source

dreamlet 0.0.51

  • Nov 10, 2022
  • in processAssays() and processOneAssay(), add argument min.prop indicating the minimum proportion of retained samples with non-zero counts

dreamlet 0.0.50

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

dreamlet 0.0.49

  • Oct 17, 2022
  • add computeCellCounts()

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

  • add totalCPM column to output of cellTypeSpecificity() to use for filtering. Functions dreamlet::plotHeatmap() plotViolin() and plotPercentBars() now ignore this column

dreamlet 0.0.45

  • update documentation

dreamlet 0.0.44

  • add plotGeneHeatmap()
  • add argument assays to plotVarPart()
  • add extractData()

dreamlet 0.0.43

  • faster aggregateToPseudoBulk() by speeding up check in .check_arg_assay()
  • more flexibility for tabToMatrix()

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

  • fix issue with aggregateToPseudoBulk() when summarizing for just 1 sample

dreamlet 0.0.38

  • add getTreat() for dreamlet() result

dreamlet 0.0.37

  • droplevels for colData in processAssays()

dreamlet 0.0.36

  • fixes in processAssays() to detect issues with SCE

dreamlet 0.0.35

  • remove old code and dependencies
  • change website theme

dreamlet 0.0.34

  • bug fix for aggregateToPseudoBulk() with sample ordering

dreamlet 0.0.33

  • bug fix for dreamletCompareClusters()

dreamlet 0.0.32

  • add colsum2() using beachmat code.

dreamlet 0.0.31

  • reduce memory usage in aggregateToPseudoBulk() by fixing `aggregateByColnames()

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

  • change return value for dreamletCompareClusters() to be compatible with zenith_gsa()
  • fix usage of formula in dreamletCompareClusters()

dreamlet 0.0.24

  • additional speed up aggregateToPseudoBulk() when a Seurat object is used
    • uses RcppEigen sparse matrix iterator

dreamlet 0.0.23

  • dramatic speed up aggregateToPseudoBulk() when a Seurat object is used
    • uses RcppEigen

dreamlet 0.0.22

  • Speed up aggregateToPseudoBulk() when a Seurat object is used

dreamlet 0.0.21

  • Add collapse=TRUE to dreamletCompareClusters()

dreamlet 0.0.20

  • Fix bug in dreamletCompareClusters()

dreamlet 0.0.19

  • Fix bug in dreamletCompareClusters()

dreamlet 0.0.18

  • add min.samples to processAssays(), processOneAssay()
  • add dreamletCompareClusters() and run_mash()
  • Fix bug in dreamletCompareClusters()
  • updated mashr dependency

dreamlet 0.0.17

  • add run_mash()
    • add zenith_gsa(), plotVolcano(), plotForest() for results
  • fix bug in cellTypeSpecificity() for genes with zero reads across all cell types
  • order of arguments in plotForest() and zenith_gsa() changed for consistancy
  • expand vignettes
  • bug fix for removeConstantTerms() when excluded variable string (i.e. tissue) is also a substring of other variables (i.e. tissueStatus)

dreamlet 0.0.16

  • add residuals() for dreamlet() result
  • add dreamletPairs()
  • fix bug in removeConstantTerms() with multiple constant terms
  • improve usability of cellTypeSpecificity() by adding plotPercentBars() and plotViolin() compatability
  • fix bug in topTable() when coef is not estimated
  • add argument assays to dreamlet(), fitVarPart(), and processAssays()

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