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37 changes: 21 additions & 16 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -19,32 +19,37 @@ Description: Utility functions for manipulating, processing, and
and more) into data tables ready for downstream analysis and data
visualization.
Depends:
R (>= 4.2.0),
R (>= 4.3.0),
QFeatures (>= 1.3.5)
Imports:
dplyr,
IHW,
ggplot2,
ggrepel,
matrixStats,
metapod,
methods,
stats,
utils,
SingleCellExperiment,
SummarizedExperiment,
MultiAssayExperiment,
MsCoreUtils,
matrixStats,
MultiAssayExperiment,
nipals,
RColorBrewer,
S4Vectors,
dplyr,
magrittr
SingleCellExperiment,
SummarizedExperiment,
stats,
tidyr,
utils
Suggests:
scpdata,
testthat,
knitr,
BiocStyle,
rmarkdown,
ggplot2,
patchwork,
impute,
knitr,
patchwork,
preprocessCore,
rmarkdown,
scater,
scpdata,
sva,
preprocessCore,
testthat,
vsn,
uwot
License: Artistic-2.0
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57 changes: 56 additions & 1 deletion NAMESPACE
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
# Generated by roxygen2: do not edit by hand

export("scpModelFilterThreshold<-")
export(aggregateFeaturesOverAssays)
export(computeSCR)
export(cumulativeSensitivityCurve)
Expand All @@ -13,27 +14,81 @@ export(readSCP)
export(readSCPfromDIANN)
export(readSingleCellExperiment)
export(reportMissingValues)
export(scpAnnotateResults)
export(scpComponentAggregate)
export(scpComponentAnalysis)
export(scpComponentBiplot)
export(scpComponentPlot)
export(scpDifferentialAggregate)
export(scpDifferentialAnalysis)
export(scpKeepEffect)
export(scpModelComponentMethods)
export(scpModelEffects)
export(scpModelFilterNPRatio)
export(scpModelFilterPlot)
export(scpModelFilterThreshold)
export(scpModelFormula)
export(scpModelInput)
export(scpModelNames)
export(scpModelResiduals)
export(scpModelWorkflow)
export(scpRemoveBatchEffect)
export(scpVarianceAggregate)
export(scpVarianceAnalysis)
export(scpVariancePlot)
export(scpVolcanoPlot)
exportClasses(ScpModel)
exportClasses(ScpModelFit)
import(QFeatures)
import(RColorBrewer)
import(SingleCellExperiment)
import(dplyr)
import(magrittr)
import(ggplot2)
importFrom(IHW,adj_pvalues)
importFrom(IHW,ihw)
importFrom(MsCoreUtils,normalize_matrix)
importFrom(MultiAssayExperiment,ExperimentList)
importFrom(MultiAssayExperiment,experiments)
importFrom(QFeatures,aggregateFeatures)
importFrom(QFeatures,readSummarizedExperiment)
importFrom(QFeatures,reduceDataFrame)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,List)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(dplyr,group_by)
importFrom(dplyr,summarise)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(matrixStats,colMedians)
importFrom(metapod,combineGroupedPValues)
importFrom(methods,as)
importFrom(methods,new)
importFrom(nipals,nipals)
importFrom(stats,as.formula)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
importFrom(stats,p.adjust)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,reformulate)
importFrom(stats,sd)
importFrom(stats,terms)
importFrom(stats,var)
importFrom(tidyr,pivot_wider)
importFrom(utils,flush.console)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
1 change: 1 addition & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

## scp 1.11.3

- Major feat: added SCP data modelling workflow + documentation
- feat: added readSCPfromDIANN() that creates a QFeatures object from
DIANN output tables.

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