Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:08:27 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for singleCellTK on merida1


To the developers/maintainers of the singleCellTK package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1856/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.6.0  (landing page)
Yichen Wang
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_15
git_last_commit: b6fc536
git_last_commit_date: 2022-04-26 11:48:48 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: singleCellTK
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.6.0.tar.gz
StartedAt: 2022-05-16 08:00:54 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 08:23:10 -0400 (Mon, 16 May 2022)
EllapsedTime: 1336.0 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/singleCellTK.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘singleCellTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    shiny     2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
plotScDblFinderResults     39.923  0.876  40.961
importExampleData          29.744  2.849  33.294
plotDoubletFinderResults   31.170  0.169  31.385
runScDblFinder             27.760  0.426  28.234
runDoubletFinder           24.220  0.085  24.453
plotTSCANPseudotimeHeatmap 24.209  0.060  24.321
plotMarkerDiffExp          13.696  0.041  13.751
plotBatchCorrCompare       13.411  0.096  13.504
plotScdsHybridResults      12.626  0.134  12.773
plotBcdsResults            11.016  0.165  11.193
plotDecontXResults         10.646  0.083  10.741
plotEmptyDropsScatter       9.613  0.028   9.664
plotEmptyDropsResults       9.556  0.032   9.610
runEmptyDrops               9.559  0.020   9.678
runDecontX                  8.600  0.061   8.675
plotDEGViolin               8.339  0.169   8.537
plotCxdsResults             8.151  0.052   8.206
detectCellOutlier           7.903  0.121   8.062
findMarkerDiffExp           7.917  0.072   8.004
plotUMAP                    7.545  0.048   7.601
plotTSCANDEgenes            7.462  0.058   7.544
findMarkerTopTable          7.246  0.042   7.296
plotDEGRegression           7.011  0.052   7.073
convertSCEToSeurat          6.540  0.189   6.764
plotClusterPseudo           6.284  0.044   6.335
plotDEGHeatmap              6.067  0.155   6.232
importGeneSetsFromMSigDB    5.530  0.400   5.942
plotTSCANPseudotimeGenes    5.760  0.025   5.803
runTSCANClusterDEAnalysis   4.993  0.019   5.017
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.



Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘singleCellTK’ ...
** using staged installation
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.355   0.080   0.412 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(singleCellTK)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum, scale, sweep


Attaching package: 'singleCellTK'

The following object is masked from 'package:BiocGenerics':

    plotPCA

> 
> test_check("singleCellTK")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 0 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Uploading data to Enrichr... Done.
  Querying HDSigDB_Human_2021... Done.
Parsing results... Done.
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels

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Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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  |======================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 390
Number of edges: 9849

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8351
Number of communities: 7
Elapsed time: 0 seconds
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 17 | SKIP 0 | PASS 162 ]

[ FAIL 0 | WARN 17 | SKIP 0 | PASS 162 ]
> 
> proc.time()
   user  system elapsed 
354.506   5.416 362.573 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0050.0030.008
SEG0.0050.0030.007
calcEffectSizes0.4200.0340.456
combineSCE3.1650.0363.213
computeZScore0.5000.0150.516
convertSCEToSeurat6.5400.1896.764
convertSeuratToSCE0.9400.0360.979
dedupRowNames0.1070.0040.110
detectCellOutlier7.9030.1218.062
diffAbundanceFET0.1430.0030.147
discreteColorPalette0.010.000.01
distinctColors0.0040.0000.004
downSampleCells1.3020.0651.368
downSampleDepth1.0460.0221.069
expData-ANY-character-method0.6360.0050.641
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.7480.0080.756
expData-set0.7340.0070.741
expData0.6430.0070.651
expDataNames-ANY-method0.7020.0060.710
expDataNames0.6460.0070.654
expDeleteDataTag0.0560.0030.058
expSetDataTag0.0420.0030.045
expTaggedData0.0450.0040.048
exportSCE0.0400.0040.045
exportSCEtoAnnData0.1600.0030.165
exportSCEtoFlatFile0.1630.0040.167
featureIndex0.0660.0040.070
findMarkerDiffExp7.9170.0728.004
findMarkerTopTable7.2460.0427.296
generateSimulatedData0.0750.0040.079
getBiomarker0.0920.0040.096
getDEGTopTable1.1900.0091.200
getDiffAbundanceResults0.0640.0010.065
getEnrichRResult0.5200.0242.150
getMSigDBTable0.0050.0020.008
getSampleSummaryStatsTable0.6160.0050.622
getSoupX0.7520.0110.764
getTSNE0.5310.0050.538
getTopHVG0.4460.0030.450
getUMAP4.7890.0344.831
importAnnData0.0020.0010.001
importBUStools0.5270.0050.535
importCellRanger2.1700.1472.324
importCellRangerV2Sample0.5950.0260.628
importCellRangerV3Sample0.7810.0140.797
importDropEst0.6990.0040.705
importExampleData29.744 2.84933.294
importGeneSetsFromCollection1.5800.1021.684
importGeneSetsFromGMT0.1100.0060.117
importGeneSetsFromList0.2490.0050.254
importGeneSetsFromMSigDB5.5300.4005.942
importMitoGeneSet0.1020.0090.111
importOptimus0.0020.0000.002
importSEQC0.5800.0180.602
importSTARsolo0.5600.0030.564
iterateSimulations0.6820.0100.692
listSampleSummaryStatsTables0.8560.0090.866
mergeSCEColData0.9180.0180.938
mouseBrainSubsetSCE0.0430.0030.046
msigdb_table0.0020.0030.005
plotBarcodeRankDropsResults1.6710.0181.691
plotBarcodeRankScatter1.3120.0081.322
plotBatchCorrCompare13.411 0.09613.504
plotBatchVariance0.5120.0060.519
plotBcdsResults11.016 0.16511.193
plotClusterAbundance1.8980.0081.912
plotClusterPseudo6.2840.0446.335
plotCxdsResults8.1510.0528.206
plotDEGHeatmap6.0670.1556.232
plotDEGRegression7.0110.0527.073
plotDEGViolin8.3390.1698.537
plotDEGVolcano1.7750.0151.797
plotDecontXResults10.646 0.08310.741
plotDimRed0.5160.0040.522
plotDoubletFinderResults31.170 0.16931.385
plotEmptyDropsResults9.5560.0329.610
plotEmptyDropsScatter9.6130.0289.664
plotMASTThresholdGenes3.2020.0233.230
plotMarkerDiffExp13.696 0.04113.751
plotPCA0.9520.0070.963
plotPathway1.7130.0121.729
plotRunPerCellQCResults0.0400.0020.041
plotSCEBarAssayData0.2510.0040.255
plotSCEBarColData0.2270.0030.231
plotSCEBatchFeatureMean0.3750.0040.381
plotSCEDensity0.3900.0050.396
plotSCEDensityAssayData0.3880.0050.394
plotSCEDensityColData0.4020.0050.408
plotSCEDimReduceColData1.5260.0151.550
plotSCEDimReduceFeatures0.8110.0060.823
plotSCEHeatmap1.3200.0091.331
plotSCEScatter0.6630.0060.669
plotSCEViolin0.4140.0040.419
plotSCEViolinAssayData0.5570.0060.563
plotSCEViolinColData0.4000.0040.406
plotScDblFinderResults39.923 0.87640.961
plotScdsHybridResults12.626 0.13412.773
plotScrubletResults0.0410.0050.045
plotSeuratElbow0.0400.0040.044
plotSeuratHVG0.0420.0030.045
plotSeuratJackStraw0.0450.0050.050
plotSeuratReduction0.0410.0040.046
plotSoupXResults0.3790.0070.386
plotTSCANDEgenes7.4620.0587.544
plotTSCANPseudotimeGenes5.7600.0255.803
plotTSCANPseudotimeHeatmap24.209 0.06024.321
plotTSCANResults4.6710.0194.700
plotTSNE1.0940.0091.105
plotTopHVG0.8770.0070.886
plotUMAP7.5450.0487.601
readSingleCellMatrix0.0080.0010.008
reportCellQC0.3840.0080.394
reportDropletQC0.0450.0080.053
reportQCTool0.3780.0060.385
retrieveSCEIndex0.0490.0080.058
runBBKNN000
runBarcodeRankDrops1.0300.0081.040
runBcds3.6770.0393.723
runCellQC0.3920.0100.404
runComBatSeq1.0350.0351.073
runCxds1.0370.0081.046
runCxdsBcdsHybrid3.8410.0393.890
runDEAnalysis1.4810.0111.495
runDecontX8.6000.0618.675
runDimReduce1.9510.0181.973
runDoubletFinder24.220 0.08524.453
runDropletQC0.0400.0040.043
runEmptyDrops9.5590.0209.678
runEnrichR0.4310.0191.621
runFastMNN3.5180.0313.565
runFeatureSelection0.4090.0010.413
runGSVA1.4300.0101.445
runKMeans0.9690.0140.987
runLimmaBC0.1530.0010.154
runMNNCorrect1.0850.0041.092
runNormalization1.1170.0071.128
runPerCellQC0.9620.0090.973
runSCANORAMA000
runSCMerge0.0060.0000.007
runScDblFinder27.760 0.42628.234
runScranSNN0.8620.0090.871
runScrublet0.0400.0040.044
runSeuratFindClusters0.0390.0050.044
runSeuratFindHVG0.0420.0040.046
runSeuratHeatmap0.0420.0040.045
runSeuratICA0.0420.0030.045
runSeuratJackStraw0.0400.0040.044
runSeuratNormalizeData0.0400.0050.045
runSeuratPCA0.0400.0020.042
runSeuratSCTransform4.8640.0644.938
runSeuratScaleData0.0420.0040.046
runSeuratUMAP0.0380.0040.042
runSingleR0.0680.0020.071
runSoupX0.3420.0040.346
runTSCAN4.1060.0224.134
runTSCANClusterDEAnalysis4.9930.0195.017
runTSCANDEG4.1400.0184.163
runVAM1.1250.0061.131
runZINBWaVE0.0050.0000.007
sampleSummaryStats0.6310.0040.636
scaterCPM0.2420.0020.244
scaterPCA1.0330.0081.041
scaterlogNormCounts0.4740.0030.480
sce0.0370.0080.046
scranModelGeneVar0.3830.0030.387
sctkListGeneSetCollections0.3530.0140.368
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv0.0000.0010.000
selectSCTKConda000
selectSCTKVirtualEnvironment0.0000.0000.001
setRowNames0.2380.0120.251
setSCTKDisplayRow0.7210.0080.730
singleCellTK0.0000.0000.001
subDiffEx0.9200.0140.935
subsetSCECols0.3510.0090.361
subsetSCERows0.8890.0080.898
summarizeSCE0.1160.0040.121
trimCounts0.4890.0070.497