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return to dependence on ARM 1.10.1 #129

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8 changes: 4 additions & 4 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,9 @@ Imports:
stats4,
graphics,
utils,
SummarizedExperiment(>= 1.5.3),
progress
SummarizedExperiment (>= 1.5.3),
progress,
arm
Depends:
SingleCellExperiment (>= 1.2.0),
R(>= 3.5)
Expand Down Expand Up @@ -73,7 +74,6 @@ Collate:
'ZlmFit-bootstrap.R'
'ZlmFit-logFC.R'
'ZlmFit.R'
'bayesglm.R'
'convertMASTClassic.R'
'ebayes-helpers.R'
'filterEval.R'
Expand All @@ -88,7 +88,7 @@ Collate:
'thresholdSCRNA.R'
'zeroinf.R'
'zlmHooks.R'
RoxygenNote: 7.0.2
RoxygenNote: 7.1.0
LazyData: true
biocViews: GeneExpression, DifferentialExpression, GeneSetEnrichment,
RNASeq, Transcriptomics, SingleCell
Expand Down
46 changes: 3 additions & 43 deletions NAMESPACE
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@@ -1,7 +1,6 @@
# Generated by roxygen2: do not edit by hand

S3method(plot,thresholdSCRNACountMatrix)
S3method(predict,ZlmFit)
S3method(print,summaryThresholdSCRNA)
S3method(print,summaryZlmFit)
S3method(summary,thresholdSCRNACountMatrix)
Expand Down Expand Up @@ -51,6 +50,7 @@ export(melt.SingleCellAssay)
export(numexp)
export(partialScore)
export(plotSCAConcordance)
export(predict.ZlmFit)
export(primerAverage)
export(read.fluidigm)
export(stat_ell)
Expand Down Expand Up @@ -86,6 +86,8 @@ importFrom(SummarizedExperiment,'rowData<-')
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(arm,bayesglm.fit)
importFrom(arm,invlogit)
importFrom(data.table,"%like%")
importFrom(data.table,":=")
importFrom(data.table,.N)
Expand Down Expand Up @@ -127,50 +129,8 @@ importFrom(plyr,ldply)
importFrom(plyr,raply)
importFrom(plyr,rbind.fill)
importFrom(reshape2,colsplit)
importFrom(stats,"contrasts<-")
importFrom(stats,.checkMFClasses)
importFrom(stats,as.formula)
importFrom(stats,binomial)
importFrom(stats,cov2cor)
importFrom(stats,delete.response)
importFrom(stats,deviance)
importFrom(stats,df.residual)
importFrom(stats,dt)
importFrom(stats,ecdf)
importFrom(stats,family)
importFrom(stats,fitted)
importFrom(stats,formula)
importFrom(stats,gaussian)
importFrom(stats,glm.control)
importFrom(stats,glm.fit)
importFrom(stats,influence)
importFrom(stats,lm.fit)
importFrom(stats,median)
importFrom(stats,model.frame)
importFrom(stats,model.matrix.default)
importFrom(stats,na.pass)
importFrom(stats,napredict)
importFrom(stats,naresid)
importFrom(stats,nobs)
importFrom(stats,offset)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(stats,qt)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,rstandard)
importFrom(stats,setNames)
importFrom(stats,sigma)
importFrom(stats,t.test)
importFrom(stats,terms)
importFrom(stats,terms.formula)
importFrom(stats,update.formula)
importFrom(stats,weighted.residuals)
importFrom(utils,read.csv)
importMethodsFrom(Biobase,fData)
importMethodsFrom(Biobase,featureData)
Expand Down
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