1. singleCellTK
  2. man
  3. exportSCE.Rd
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Fix CellQCReport bug. Add importAlevin function. Add exportSCEToSeurat function

rz2333 authored on 17/04/2021 19:30:28
Showing 1 changed files
man/exportSCE.Rd
History View file @ 6e7955a8
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@@ -9,7 +9,7 @@ exportSCE(
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   samplename = "sample",
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   directory = "./",
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   type = "Cells",
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-  format = c("SCE", "AnnData", "FlatFile", "HTAN")
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+  format = c("SCE", "AnnData", "FlatFile", "HTAN", "Seurat")
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 )
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 }
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 \arguments{
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Integrate changes from sctk_qc_1.7.6. Fix bugs in QC and QC report. Fix bugs of vapply

rz2333 authored on 17/10/2020 00:43:30
Showing 1 changed files
man/exportSCE.Rd
History View file @ 3bcd1a4a
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@@ -28,12 +28,15 @@ It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}
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 \item{format}{The format of output. It currently supports flat files, rds files
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 and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").}
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 }
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-<<<<<<< HEAD
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-=======
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 \value{
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 Generates a file containing data from \code{inSCE}, in specified \code{format}.
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 }
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->>>>>>> compbiomed-master
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 \description{
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 Export data in SingleCellExperiment object
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 }
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+\examples{
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+data(scExample)
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+\dontrun{
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+exportSCE(sce, format = "SCE")
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+}
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+}
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Merge from upstream

rz2333 authored on 16/10/2020 03:13:00
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Merge from upstream

rz2333 authored on 16/10/2020 03:10:12
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Remove '@' in example code

Yusuke Koga authored on 16/10/2020 02:16:22
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man/exportSCE.Rd
History View file @ 63039a6a
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@@ -29,7 +29,7 @@ It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}
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 and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").}
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 }
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 \value{
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-Generates a file containing data from \code{inSCE} as \code{format}.
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+Generates a file containing data from \code{inSCE}, in specified \code{format}.
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 }
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 \description{
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 Export data in SingleCellExperiment object
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Merge branch 'master' of https://github.com/compbiomed/singleCellTK

Joshua D. Campbell authored on 16/10/2020 01:50:26
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doc fix

Joshua D. Campbell authored on 16/10/2020 01:50:21
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man/exportSCE.Rd
History View file @ 62ce0544
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@@ -31,3 +31,9 @@ and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData"
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 \description{
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 Export data in SingleCellExperiment object
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 }
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+\examples{
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+data(scExample)
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+\dontrun{
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+exportSCE(sce, format = "SCE")
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+}
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+}
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Merge upstream

Yusuke Koga authored on 16/10/2020 01:47:26
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Put dontrun around examples that were outputting files. Removed Remotes from DESCRIPTION. Further compressed data objects

Joshua D. Campbell authored on 16/10/2020 00:52:57
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man/exportSCE.Rd
History View file @ c802b90f
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@@ -31,6 +31,3 @@ and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData"
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 \description{
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 Export data in SingleCellExperiment object
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 }
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-\examples{
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-exportSCE(mouseBrainSubsetSCE, format = "SCE")
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-}
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Merge branch 'master' of github.com:compbiomed/singleCellTK

Yusuke Koga authored on 16/10/2020 00:27:01
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Add Runnable functions

Yusuke Koga authored on 15/10/2020 16:44:51
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man/exportSCE.Rd
History View file @ 0ccddee1
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@@ -31,3 +31,6 @@ and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData"
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 \description{
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 Export data in SingleCellExperiment object
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 }
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+\examples{
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+exportSCE(mouseBrainSubsetSCE, format = "SCE")
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+}
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Update documentation

Yusuke Koga authored on 12/10/2020 20:59:18
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man/exportSCE.Rd
History View file @ ea450967
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@@ -13,8 +13,8 @@ exportSCE(
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 )
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 }
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 \arguments{
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-\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object
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-that contains the data. QC metrics are stored in colData of the
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+\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object
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+that contains the data. QC metrics are stored in colData of the
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 singleCellExperiment object.}
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 \item{samplename}{Sample name. This will be used as name of subdirectories
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@@ -22,7 +22,7 @@ and the prefix of flat file output. Default is 'sample'.}
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 \item{directory}{Output directory. Default is './'.}
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-\item{type}{Type of data. The type of data stored in SingleCellExperiment object.
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+\item{type}{Type of data. The type of data stored in SingleCellExperiment object.
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 It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}
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 \item{format}{The format of output. It currently supports flat files, rds files
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Updated description in DESCRIPTION. Moved importMultipleSources to its own file and removed some shiny code. Updated docs.

Joshua D. Campbell authored on 12/10/2020 18:25:27
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man/exportSCE.Rd
History View file @ 31390a70
... ... 
@@ -13,8 +13,8 @@ exportSCE(
13 13 
 )
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 }
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 \arguments{
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-\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object
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-that contains the data. QC metrics are stored in colData of the
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+\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object
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+that contains the data. QC metrics are stored in colData of the
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 singleCellExperiment object.}
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 \item{samplename}{Sample name. This will be used as name of subdirectories
... ... 
@@ -22,7 +22,7 @@ and the prefix of flat file output. Default is 'sample'.}
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 \item{directory}{Output directory. Default is './'.}
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-\item{type}{Type of data. The type of data stored in SingleCellExperiment object.
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+\item{type}{Type of data. The type of data stored in SingleCellExperiment object.
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 It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}
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28 28 
 \item{format}{The format of output. It currently supports flat files, rds files
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Update QC report and edited output format of SCTK QC pipeline

rz2333 authored on 10/09/2020 16:26:11
Showing 1 changed files
man/exportSCE.Rd
History View file @ 0df1d56e
... ... 
@@ -9,7 +9,7 @@ exportSCE(
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   samplename = "sample",
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   directory = "./",
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   type = "Cells",
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-  format = c("R", "Python", "FlatFile", "HTAN")
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+  format = c("SCE", "AnnData", "FlatFile", "HTAN")
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 )
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 }
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 \arguments{
... ... 
@@ -26,7 +26,7 @@ and the prefix of flat file output. Default is 'sample'.}
26 26 
 It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}
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28 28 
 \item{format}{The format of output. It currently supports flat files, rds files
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-and python h5 files. It can output multiple formats. Default: c('R', 'Python', 'Flatfile').}
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+and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").}
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 }
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 \description{
32 32 
 Export data in SingleCellExperiment object
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Update documentation of sctkQCUtils.R

rz2333 authored on 26/05/2020 19:18:06
Showing 1 changed files
man/exportSCE.Rd
History View file @ f5e1db0c
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@@ -9,7 +9,7 @@ exportSCE(
9 9 
   samplename = "sample",
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   directory = "./",
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   type = "Cells",
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-  format = c("R", "Python", "FlatFile")
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+  format = c("R", "Python", "FlatFile", "HTAN")
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 )
14 14 
 }
15 15 
 \arguments{
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Organize SCTK_runQC.R and move utility functions into R/sctkQCUtils.R

rz2333 authored on 25/05/2020 17:23:03
Showing 1 changed files
man/exportSCE.Rd
History View file @ ece1f3d8
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new file mode 100644
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@@ -0,0 +1,33 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/sctkQCUtils.R
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+\name{exportSCE}
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+\alias{exportSCE}
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+\title{Export data in SingleCellExperiment object}
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+\usage{
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+exportSCE(
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+  inSCE,
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+  samplename = "sample",
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+  directory = "./",
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+  type = "Cells",
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+  format = c("R", "Python", "FlatFile")
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+)
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+}
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+\arguments{
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+\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object
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+that contains the data. QC metrics are stored in colData of the
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+singleCellExperiment object.}
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+
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+\item{samplename}{Sample name. This will be used as name of subdirectories
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+and the prefix of flat file output. Default is 'sample'.}
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+
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+\item{directory}{Output directory. Default is './'.}
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+
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+\item{type}{Type of data. The type of data stored in SingleCellExperiment object.
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+It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}
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+
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+\item{format}{The format of output. It currently supports flat files, rds files
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+and python h5 files. It can output multiple formats. Default: c('R', 'Python', 'Flatfile').}
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+}
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+\description{
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+Export data in SingleCellExperiment object
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+}