NEWS.md

In GabrielHoffman/dreamlet: Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

dreamlet 1.4.0

• Nov 5, 2024
• update to Bioc 3.20

dreamlet 1.3.4

• Oct 27, 2024
• Better error reporting addressing https://github.com/GabrielHoffman/dreamlet/issues/25

dreamlet 1.3.3

• July 19, 2024
• fix in .read_matrix_block()
• See https://github.com/GabrielHoffman/dreamlet/pull/23/commits/c453ac98ebc0329279b4dd3ae26a674df0e9b1f2

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
  • from https://github.com/GabrielHoffman/dreamlet/issues/18

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 https://github.com/GabrielHoffman/dreamlet/issues/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

• May 24, 2023
• required zellkonverter (>= 1.10.1) to avoid issues with previous version
  • issue solved by https://github.com/theislab/zellkonverter/blob/b56718d113327020c024e188d9ac67ea57eaf35d/R/AnnData2SCE.R#L351

dreamlet 0.99.11

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

dreamlet 0.99.10

• April 24, 2023
• Fix issue in raised in Bioconductor submission: https://github.com/Bioconductor/Contributions/issues/2955#issuecomment-1498070980
• Compatibility with variancePartition v2.0.0

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

• March 20, 2023
• fix Biocondcutor submission based on https://github.com/Bioconductor/Contributions/issues/2955#issuecomment-1476037237

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

GabrielHoffman/dreamlet documentation built on Nov. 8, 2024, 2:45 a.m.