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Change from Imports to Suggests #396

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Mar 14, 2024
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Change from Imports to Suggests #396

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3 changes: 2 additions & 1 deletion src/R/packages/DropSeq.dropulation/DESCRIPTION
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Expand Up @@ -4,7 +4,8 @@ Title: Tools for analyzing Dropulation data
Version: 3.0.0
Date: 2024-03-13
Imports: graphics, utils, stats, data.table,RColorBrewer,vegan, gridExtra,
ggplot2,ggrepel,purrr,stringr,scales,DropSeq.utilities
ggplot2,ggrepel,purrr,stringr,scales
Suggests: DropSeq.utilities
Remotes: github::broadinstitute/Drop-seq/src/R/packages/DropSeq.utilities
Author: Jim Nemesh
Maintainer: McCarroll Lab <[email protected]>
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1 change: 0 additions & 1 deletion src/R/packages/DropSeq.dropulation/NAMESPACE
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Expand Up @@ -4,7 +4,6 @@ export(censusSeqQC)
export(donorAssignmentQC)
export(estimateDoubletRatePoissonDistribution)
export(estimateEmptyCount)
import(DropSeq.utilities)
import(RColorBrewer)
import(data.table)
import(ggplot2)
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3 changes: 2 additions & 1 deletion src/R/packages/DropSeq.dropulation/R/DonorAssignmentStandardAnalysis.R
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Expand Up @@ -602,7 +602,8 @@ writeSummaryStats<-function (summaryStats, outSummaryStatsFile) {
#' @param outCellBarcodesFile cell barcodes for donors in the experiment (optional)
#' @param anonymizeDonors If set to true, donor IDs are changed to DONOR_1, DONOR_2, etc. Purely for sharing
#' visualizations of not-yet-public data.
#' @import grDevices graphics utils stats data.table RColorBrewer DropSeq.utilities vegan
#' @import grDevices graphics utils stats data.table RColorBrewer vegan
#' @suggest DropSeq.utilities
#' @export
donorAssignmentQC<-function (expName="", likelihoodSummaryFile, doubletLikelihoodFile, dgeSummaryFile=NULL, dgeRawSummaryFile=NULL,
readsPerCellFile=NULL, censusFile=NULL, expectedSamplesFile, outFileLikelyDonors=NULL, outDonorToCellMap=NULL, outPDF=NULL,
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4 changes: 4 additions & 0 deletions src/R/packages/DropSeq.dropulation/README.md
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Expand Up @@ -19,3 +19,7 @@ It is not recommended to install the latest version of DropSeq.dropulation from
# install.packages("devtools")
devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.dropulation")
```

Note that dependent package DropSeq.utilities is Suggests: rather than Imports: in order
to make it less likely that a user will install a possibly-unstable version of that package
rather than a released version.
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