Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1977/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.16.0  (landing page)
Joshua David Campbell
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_20
git_last_commit: 6bbe76f
git_last_commit_date: 2024-10-29 11:30:33 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for singleCellTK on kunpeng2

To the developers/maintainers of the singleCellTK package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: singleCellTK
Version: 2.16.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings singleCellTK_2.16.0.tar.gz
StartedAt: 2024-11-20 12:33:01 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 12:53:25 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 1224.1 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings singleCellTK_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/singleCellTK.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.16.0’
* 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  7.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   1.6Mb
    shiny     3.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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   46.789  0.291  45.414
runSeuratSCTransform     45.465  0.514  46.148
plotDoubletFinderResults 42.285  0.296  42.537
runDoubletFinder         38.272  0.171  38.455
runScDblFinder           32.029  0.423  30.753
importExampleData        17.067  1.234  24.173
plotBatchCorrCompare     14.599  0.399  15.013
plotScdsHybridResults    11.884  0.087  10.879
plotBcdsResults          10.567  0.295   9.790
plotDecontXResults        9.178  0.191   9.277
plotCxdsResults           8.074  0.040   8.124
runUMAP                   7.952  0.046   8.007
runDecontX                7.893  0.048   7.954
plotUMAP                  7.662  0.024   7.692
detectCellOutlier         6.592  0.407   7.015
plotDEGViolin             6.098  0.080   6.192
plotFindMarkerHeatmap     5.738  0.076   5.826
convertSCEToSeurat        5.597  0.136   5.743
plotEmptyDropsScatter     5.619  0.048   5.674
plotEmptyDropsResults     5.554  0.032   5.593
runEmptyDrops             5.243  0.008   5.259
plotTSCANClusterDEG       5.109  0.032   5.153
plotDEGRegression         4.835  0.188   5.035
getEnrichRResult          0.474  0.127  15.635
runEnrichR                0.428  0.017  39.585
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.

Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  0.289   0.015   0.203

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, 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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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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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.
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
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  |======================================================================| 100%

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  |======================================================================| 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
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

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  |======================================================================| 100%

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  |======================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 20 | SKIP 0 | PASS 224 ]

[ FAIL 0 | WARN 20 | SKIP 0 | PASS 224 ]
> 
> proc.time()
   user  system elapsed 
333.033   7.033 353.574

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0000.003
SEG0.0030.0000.003
calcEffectSizes0.2380.0080.247
combineSCE1.0120.0281.041
computeZScore0.3060.0360.343
convertSCEToSeurat5.5970.1365.743
convertSeuratToSCE0.4570.0000.457
dedupRowNames0.0730.0000.073
detectCellOutlier6.5920.4077.015
diffAbundanceFET0.0660.0000.067
discreteColorPalette0.0080.0000.007
distinctColors0.0020.0000.003
downSampleCells0.7330.0560.790
downSampleDepth0.6240.0000.625
expData-ANY-character-method0.1680.0000.169
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.2180.0000.219
expData-set0.2050.0000.205
expData0.170.000.17
expDataNames-ANY-method0.1590.0000.160
expDataNames0.1550.0040.161
expDeleteDataTag0.0410.0040.046
expSetDataTag0.0350.0000.034
expTaggedData0.0300.0040.033
exportSCE0.0290.0000.029
exportSCEtoAnnData0.0760.0120.088
exportSCEtoFlatFile0.1100.0040.114
featureIndex0.0460.0000.047
generateSimulatedData0.0660.0000.066
getBiomarker0.0740.0000.074
getDEGTopTable0.9210.0040.927
getDiffAbundanceResults0.0620.0000.062
getEnrichRResult 0.474 0.12715.635
getFindMarkerTopTable2.1420.1322.279
getMSigDBTable0.0040.0000.005
getPathwayResultNames0.0350.0000.035
getSampleSummaryStatsTable0.2560.0200.277
getSoupX000
getTSCANResults1.4420.0921.537
getTopHVG1.1840.0001.186
importAnnData0.0020.0000.001
importBUStools0.2810.0000.284
importCellRanger1.1060.0031.117
importCellRangerV2Sample0.2170.0000.217
importCellRangerV3Sample0.4020.0070.411
importDropEst0.3240.0080.334
importExampleData17.067 1.23424.173
importGeneSetsFromCollection2.5240.0522.582
importGeneSetsFromGMT0.0850.0040.089
importGeneSetsFromList0.1760.0000.177
importGeneSetsFromMSigDB3.0780.1403.225
importMitoGeneSet0.0790.0080.086
importOptimus0.0000.0020.003
importSEQC0.2110.0650.278
importSTARsolo0.2220.0270.252
iterateSimulations0.2410.0640.306
listSampleSummaryStatsTables0.3770.0640.441
mergeSCEColData0.7680.1560.926
mouseBrainSubsetSCE0.050.000.05
msigdb_table0.0020.0000.002
plotBarcodeRankDropsResults0.8870.0710.961
plotBarcodeRankScatter0.8940.0240.920
plotBatchCorrCompare14.599 0.39915.013
plotBatchVariance0.4360.0160.452
plotBcdsResults10.567 0.295 9.790
plotBubble0.8670.0320.902
plotClusterAbundance1.2610.0161.279
plotCxdsResults8.0740.0408.124
plotDEGHeatmap2.9840.0603.052
plotDEGRegression4.8350.1885.035
plotDEGViolin6.0980.0806.192
plotDEGVolcano1.1530.0041.159
plotDecontXResults9.1780.1919.277
plotDimRed0.2570.0000.258
plotDoubletFinderResults42.285 0.29642.537
plotEmptyDropsResults5.5540.0325.593
plotEmptyDropsScatter5.6190.0485.674
plotFindMarkerHeatmap5.7380.0765.826
plotMASTThresholdGenes1.9060.0471.958
plotPCA0.4320.0000.433
plotPathway0.7340.0120.748
plotRunPerCellQCResults2.8340.0002.841
plotSCEBarAssayData0.3210.0000.322
plotSCEBarColData0.2120.0000.212
plotSCEBatchFeatureMean0.3120.0000.313
plotSCEDensity0.2960.0040.301
plotSCEDensityAssayData0.2300.0000.231
plotSCEDensityColData0.2900.0000.291
plotSCEDimReduceColData0.7180.0000.719
plotSCEDimReduceFeatures0.3820.0000.383
plotSCEHeatmap0.6660.0110.679
plotSCEScatter0.3480.0000.348
plotSCEViolin0.3460.0000.347
plotSCEViolinAssayData0.3540.0000.355
plotSCEViolinColData0.3390.0000.339
plotScDblFinderResults46.789 0.29145.414
plotScanpyDotPlot0.0320.0000.032
plotScanpyEmbedding0.0320.0000.032
plotScanpyHVG0.0270.0040.031
plotScanpyHeatmap0.0320.0000.032
plotScanpyMarkerGenes0.0310.0000.031
plotScanpyMarkerGenesDotPlot0.0310.0000.032
plotScanpyMarkerGenesHeatmap0.0320.0000.032
plotScanpyMarkerGenesMatrixPlot0.0330.0000.034
plotScanpyMarkerGenesViolin0.0330.0000.034
plotScanpyMatrixPlot0.0330.0000.033
plotScanpyPCA0.0340.0000.033
plotScanpyPCAGeneRanking0.0370.0000.037
plotScanpyPCAVariance0.0370.0000.037
plotScanpyViolin0.030.000.03
plotScdsHybridResults11.884 0.08710.879
plotScrubletResults0.0280.0000.029
plotSeuratElbow0.0280.0000.028
plotSeuratHVG0.0280.0000.028
plotSeuratJackStraw0.0290.0000.029
plotSeuratReduction0.0280.0000.029
plotSoupXResults000
plotTSCANClusterDEG5.1090.0325.153
plotTSCANClusterPseudo1.6820.0041.690
plotTSCANDimReduceFeatures1.7430.0001.748
plotTSCANPseudotimeGenes2.0270.0002.031
plotTSCANPseudotimeHeatmap1.8930.0081.906
plotTSCANResults1.6110.0041.618
plotTSNE0.4350.0000.436
plotTopHVG0.7930.0080.803
plotUMAP7.6620.0247.692
readSingleCellMatrix0.0060.0000.006
reportCellQC0.1060.0000.107
reportDropletQC0.0280.0000.028
reportQCTool0.1070.0000.107
retrieveSCEIndex0.0360.0000.036
runBBKNN000
runBarcodeRankDrops0.2890.0000.289
runBcds3.0410.0162.004
runCellQC0.1080.0000.108
runClusterSummaryMetrics0.4990.0040.504
runComBatSeq0.7300.0000.732
runCxds0.4490.0000.450
runCxdsBcdsHybrid3.1020.0202.032
runDEAnalysis0.4850.0040.490
runDecontX7.8930.0487.954
runDimReduce0.3580.0040.363
runDoubletFinder38.272 0.17138.455
runDropletQC0.0270.0000.027
runEmptyDrops5.2430.0085.259
runEnrichR 0.428 0.01739.585
runFastMNN3.1570.1722.627
runFeatureSelection0.3290.0040.335
runFindMarker2.1480.0562.209
runGSVA1.0320.0241.059
runHarmony0.0530.0000.054
runKMeans0.2340.0000.235
runLimmaBC0.1060.0000.107
runMNNCorrect0.5520.0080.561
runModelGeneVar0.4270.0000.428
runNormalization2.9450.1003.051
runPerCellQC0.4890.0120.503
runSCANORAMA000
runSCMerge0.0040.0000.005
runScDblFinder32.029 0.42330.753
runScanpyFindClusters0.030.000.03
runScanpyFindHVG0.0320.0000.032
runScanpyFindMarkers0.0330.0000.033
runScanpyNormalizeData0.1420.0080.150
runScanpyPCA0.0310.0000.031
runScanpyScaleData0.0300.0000.031
runScanpyTSNE0.0280.0040.031
runScanpyUMAP0.0330.0000.034
runScranSNN0.4060.0200.427
runScrublet0.0290.0000.029
runSeuratFindClusters0.0300.0000.031
runSeuratFindHVG0.6160.0640.683
runSeuratHeatmap0.0260.0000.026
runSeuratICA0.0220.0040.027
runSeuratJackStraw0.0260.0000.026
runSeuratNormalizeData0.0270.0000.027
runSeuratPCA0.0280.0000.028
runSeuratSCTransform45.465 0.51446.148
runSeuratScaleData0.0340.0000.034
runSeuratUMAP0.0310.0000.031
runSingleR0.0480.0000.048
runSoupX000
runTSCAN0.9170.0000.917
runTSCANClusterDEAnalysis1.0430.0001.045
runTSCANDEG0.9650.0040.971
runTSNE1.1870.0041.089
runUMAP7.9520.0468.007
runVAM0.4410.0000.442
runZINBWaVE0.0050.0000.005
sampleSummaryStats0.2320.0000.233
scaterCPM0.1460.0000.146
scaterPCA0.6010.0000.603
scaterlogNormCounts0.2770.0080.286
sce0.0240.0000.024
sctkListGeneSetCollections0.0950.0000.095
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv0.0010.0000.000
selectSCTKConda000
selectSCTKVirtualEnvironment000
setRowNames0.1050.0000.105
setSCTKDisplayRow0.3810.0000.381
singleCellTK0.0010.0000.000
subDiffEx0.3870.0040.391
subsetSCECols0.10.00.1
subsetSCERows0.2680.0000.268
summarizeSCE0.0810.0000.081
trimCounts0.2540.0040.258