Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-28 17:44 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 1992/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.14.0  (landing page)
Joshua David Campbell
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_19
git_last_commit: cd29b84
git_last_commit_date: 2024-04-30 11:06:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped

CHECK results for singleCellTK on merida1

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.

raw results


Summary

Package: singleCellTK
Version: 2.14.0
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_2.14.0.tar.gz
StartedAt: 2024-06-27 12:01:46 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 12:35:09 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 2002.7 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_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.14.0’
* 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  6.8Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   1.5Mb
    shiny     2.9Mb
* 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 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 ... NOTE
checkRd: (-1) dedupRowNames.Rd:10: Lost braces
    10 | \item{x}{A matrix like or /linkS4class{SingleCellExperiment} object, on which
       |                                       ^
checkRd: (-1) dedupRowNames.Rd:14: Lost braces
    14 | /linkS4class{SingleCellExperiment} object. When set to \code{TRUE}, will
       |             ^
checkRd: (-1) dedupRowNames.Rd:22: Lost braces
    22 | By default, a matrix or /linkS4class{SingleCellExperiment} object
       |                                     ^
checkRd: (-1) dedupRowNames.Rd:24: Lost braces
    24 | When \code{x} is a /linkS4class{SingleCellExperiment} and \code{as.rowData}
       |                                ^
checkRd: (-1) plotBubble.Rd:42: Lost braces
    42 | \item{scale}{Option to scale the data. Default: /code{FALSE}. Selected assay will not be scaled.}
       |                                                      ^
checkRd: (-1) runClusterSummaryMetrics.Rd:27: Lost braces
    27 | \item{scale}{Option to scale the data. Default: /code{FALSE}. Selected assay will not be scaled.}
       |                                                      ^
checkRd: (-1) runEmptyDrops.Rd:66: Lost braces
    66 | provided \\linkS4class{SingleCellExperiment} object.
       |                       ^
checkRd: (-1) runSCMerge.Rd:44: Lost braces
    44 | construct pseudo-replicates. The length of code{kmeansK} needs to be the same
       |                                                ^
* 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     50.368  1.235  63.529
plotDoubletFinderResults   47.221  0.480  53.781
runDoubletFinder           41.884  0.305  48.910
runScDblFinder             33.190  0.560  38.724
importExampleData          27.578  2.810  34.878
plotBatchCorrCompare       15.236  0.240  18.160
plotScdsHybridResults      14.008  0.184  16.958
plotTSCANClusterDEG        13.320  0.203  16.254
plotBcdsResults            12.717  0.412  15.127
plotDecontXResults         12.742  0.158  14.539
plotFindMarkerHeatmap      12.206  0.097  14.286
plotDEGViolin              11.209  0.219  13.180
plotEmptyDropsResults      10.620  0.089  12.279
plotEmptyDropsScatter      10.604  0.084  12.186
detectCellOutlier           9.791  0.205  11.290
runEmptyDrops               9.896  0.070  11.798
plotCxdsResults             9.787  0.149  11.403
runSeuratSCTransform        9.654  0.147  11.789
convertSCEToSeurat          9.374  0.350  11.137
plotDEGRegression           9.425  0.147  10.628
runDecontX                  9.268  0.086  10.858
getFindMarkerTopTable       8.701  0.092  10.022
runFindMarker               8.529  0.095  10.022
runUMAP                     8.530  0.090  10.037
plotUMAP                    8.495  0.097   9.953
plotDEGHeatmap              7.505  0.181   8.821
plotTSCANPseudotimeHeatmap  5.824  0.056   6.835
plotTSCANDimReduceFeatures  5.819  0.059   7.070
plotTSCANClusterPseudo      5.775  0.060   6.928
plotTSCANPseudotimeGenes    5.550  0.055   6.717
plotTSCANResults            5.464  0.067   6.550
plotRunPerCellQCResults     5.459  0.056   6.572
importGeneSetsFromMSigDB    4.873  0.182   5.518
getTSCANResults             4.404  0.074   5.056
runFastMNN                  4.209  0.086   5.035
getEnrichRResult            0.741  0.059  11.898
runEnrichR                  0.683  0.041   6.305
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  0.378   0.121   0.486

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, 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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  |======================================================================| 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%
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
No annotation package name available in the input data object.
Attempting to directly match identifiers in data to gene sets.
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels

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No annotation package name available in the input data object.
Attempting to directly match identifiers in data to gene sets.
Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels

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Performing log-normalization
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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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  |======================================================================| 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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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...
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8351
Number of communities: 7
Elapsed time: 0 seconds
Using method 'umap'
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 21 | SKIP 0 | PASS 224 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 224 ]
> 
> proc.time()
   user  system elapsed 
485.509  11.024 573.313

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0040.0050.010
SEG0.0040.0040.010
calcEffectSizes0.5080.0580.644
combineSCE3.5650.1384.194
computeZScore0.4640.0220.544
convertSCEToSeurat 9.374 0.35011.137
convertSeuratToSCE1.2050.0161.380
dedupRowNames0.1260.0100.149
detectCellOutlier 9.791 0.20511.290
diffAbundanceFET0.1040.0100.123
discreteColorPalette0.0120.0010.013
distinctColors0.0050.0010.007
downSampleCells1.4300.1541.775
downSampleDepth1.2560.0631.478
expData-ANY-character-method0.7370.0110.842
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.8000.0130.926
expData-set0.8550.0100.978
expData0.7690.0650.932
expDataNames-ANY-method0.7950.0820.983
expDataNames0.7300.0100.822
expDeleteDataTag0.0720.0050.089
expSetDataTag0.0470.0050.055
expTaggedData0.0570.0040.068
exportSCE0.0600.0070.077
exportSCEtoAnnData0.1410.0040.163
exportSCEtoFlatFile0.1390.0040.161
featureIndex0.070.010.09
generateSimulatedData0.1010.0090.123
getBiomarker0.1220.0080.154
getDEGTopTable2.1250.0592.419
getDiffAbundanceResults0.0980.0080.122
getEnrichRResult 0.741 0.05911.898
getFindMarkerTopTable 8.701 0.09210.022
getMSigDBTable0.0080.0070.016
getPathwayResultNames0.0450.0060.058
getSampleSummaryStatsTable0.7720.0080.880
getSoupX0.0010.0000.001
getTSCANResults4.4040.0745.056
getTopHVG2.6540.0303.006
importAnnData0.0030.0020.004
importBUStools0.6400.0080.752
importCellRanger2.7560.0643.170
importCellRangerV2Sample0.6830.0060.765
importCellRangerV3Sample1.0110.0261.158
importDropEst0.7550.0080.850
importExampleData27.578 2.81034.878
importGeneSetsFromCollection1.6810.1411.956
importGeneSetsFromGMT0.1310.0100.151
importGeneSetsFromList0.2900.0100.324
importGeneSetsFromMSigDB4.8730.1825.518
importMitoGeneSet0.1170.0120.142
importOptimus0.0030.0010.004
importSEQC0.6640.0340.862
importSTARsolo0.6500.0090.739
iterateSimulations0.8110.0160.947
listSampleSummaryStatsTables0.9620.0201.244
mergeSCEColData1.1300.0341.475
mouseBrainSubsetSCE0.0660.0100.083
msigdb_table0.0030.0040.007
plotBarcodeRankDropsResults2.0000.0362.304
plotBarcodeRankScatter2.1820.0222.484
plotBatchCorrCompare15.236 0.24018.160
plotBatchVariance0.8190.0721.040
plotBcdsResults12.717 0.41215.127
plotBubble2.5340.1033.143
plotClusterAbundance2.1570.0282.490
plotCxdsResults 9.787 0.14911.403
plotDEGHeatmap7.5050.1818.821
plotDEGRegression 9.425 0.14710.628
plotDEGViolin11.209 0.21913.180
plotDEGVolcano2.4650.0332.824
plotDecontXResults12.742 0.15814.539
plotDimRed0.6470.0110.734
plotDoubletFinderResults47.221 0.48053.781
plotEmptyDropsResults10.620 0.08912.279
plotEmptyDropsScatter10.604 0.08412.186
plotFindMarkerHeatmap12.206 0.09714.286
plotMASTThresholdGenes4.1300.0594.874
plotPCA1.1580.0191.406
plotPathway2.1160.0312.576
plotRunPerCellQCResults5.4590.0566.572
plotSCEBarAssayData0.4560.0110.551
plotSCEBarColData0.3770.0110.472
plotSCEBatchFeatureMean0.5610.0070.664
plotSCEDensity0.5870.0140.752
plotSCEDensityAssayData0.4080.0110.581
plotSCEDensityColData0.5160.0150.845
plotSCEDimReduceColData1.8010.0272.137
plotSCEDimReduceFeatures0.9900.0171.193
plotSCEHeatmap1.6780.0202.009
plotSCEScatter0.8940.0151.095
plotSCEViolin0.6120.0140.731
plotSCEViolinAssayData0.7100.0160.845
plotSCEViolinColData0.5910.0120.725
plotScDblFinderResults50.368 1.23563.529
plotScanpyDotPlot0.0430.0050.057
plotScanpyEmbedding0.0430.0050.060
plotScanpyHVG0.0440.0070.059
plotScanpyHeatmap0.0420.0060.054
plotScanpyMarkerGenes0.0500.0050.089
plotScanpyMarkerGenesDotPlot0.0430.0050.058
plotScanpyMarkerGenesHeatmap0.0430.0040.060
plotScanpyMarkerGenesMatrixPlot0.0430.0100.062
plotScanpyMarkerGenesViolin0.0450.0050.061
plotScanpyMatrixPlot0.0510.0030.068
plotScanpyPCA0.0480.0040.061
plotScanpyPCAGeneRanking0.0500.0050.071
plotScanpyPCAVariance0.0420.0040.051
plotScanpyViolin0.0500.0070.071
plotScdsHybridResults14.008 0.18416.958
plotScrubletResults0.0420.0040.055
plotSeuratElbow0.0450.0050.059
plotSeuratHVG0.0480.0040.065
plotSeuratJackStraw0.0420.0050.055
plotSeuratReduction0.0440.0050.059
plotSoupXResults0.0000.0000.001
plotTSCANClusterDEG13.320 0.20316.254
plotTSCANClusterPseudo5.7750.0606.928
plotTSCANDimReduceFeatures5.8190.0597.070
plotTSCANPseudotimeGenes5.5500.0556.717
plotTSCANPseudotimeHeatmap5.8240.0566.835
plotTSCANResults5.4640.0676.550
plotTSNE1.2820.0221.497
plotTopHVG1.2360.0271.466
plotUMAP8.4950.0979.953
readSingleCellMatrix0.0100.0020.019
reportCellQC0.4220.0090.498
reportDropletQC0.0490.0050.061
reportQCTool0.4320.0110.520
retrieveSCEIndex0.0600.0050.079
runBBKNN0.0000.0010.001
runBarcodeRankDrops0.9800.0111.152
runBcds3.8260.0644.480
runCellQC0.4170.0090.493
runClusterSummaryMetrics1.7720.0482.096
runComBatSeq1.0280.0261.270
runCxds1.1150.0181.316
runCxdsBcdsHybrid3.9450.0724.647
runDEAnalysis1.6960.0472.053
runDecontX 9.268 0.08610.858
runDimReduce1.0980.0131.294
runDoubletFinder41.884 0.30548.910
runDropletQC0.0440.0050.057
runEmptyDrops 9.896 0.07011.798
runEnrichR0.6830.0416.305
runFastMNN4.2090.0865.035
runFeatureSelection0.4810.0090.569
runFindMarker 8.529 0.09510.022
runGSVA2.0260.0642.466
runHarmony0.0910.0020.103
runKMeans1.0850.0191.296
runLimmaBC0.1910.0020.223
runMNNCorrect1.3320.0171.571
runModelGeneVar1.1080.0131.280
runNormalization3.2560.0453.822
runPerCellQC1.220.021.43
runSCANORAMA0.0000.0010.001
runSCMerge0.0070.0010.010
runScDblFinder33.190 0.56038.724
runScanpyFindClusters0.0480.0080.071
runScanpyFindHVG0.0420.0050.052
runScanpyFindMarkers0.0440.0040.055
runScanpyNormalizeData0.4870.0100.566
runScanpyPCA0.0440.0040.056
runScanpyScaleData0.0430.0070.066
runScanpyTSNE0.0440.0060.091
runScanpyUMAP0.0430.0050.067
runScranSNN1.8190.0302.154
runScrublet0.0410.0030.066
runSeuratFindClusters0.0410.0030.052
runSeuratFindHVG1.8970.1232.347
runSeuratHeatmap0.0460.0050.056
runSeuratICA0.0460.0050.060
runSeuratJackStraw0.0500.0040.062
runSeuratNormalizeData0.0460.0040.056
runSeuratPCA0.0470.0030.061
runSeuratSCTransform 9.654 0.14711.789
runSeuratScaleData0.0420.0050.053
runSeuratUMAP0.0430.0060.056
runSingleR0.0850.0050.107
runSoupX0.0000.0010.001
runTSCAN3.7260.0504.389
runTSCANClusterDEAnalysis3.9100.0424.527
runTSCANDEG3.7780.0484.487
runTSNE1.7650.0262.084
runUMAP 8.530 0.09010.037
runVAM1.3560.0181.564
runZINBWaVE0.0070.0020.009
sampleSummaryStats0.7240.0110.833
scaterCPM0.2390.0060.284
scaterPCA1.6110.0201.863
scaterlogNormCounts0.4930.0080.585
sce0.0420.0070.059
sctkListGeneSetCollections0.1780.0100.215
sctkPythonInstallConda0.0000.0010.001
sctkPythonInstallVirtualEnv0.0010.0000.001
selectSCTKConda0.0000.0010.001
selectSCTKVirtualEnvironment0.0000.0010.003
setRowNames0.3050.0190.376
setSCTKDisplayRow0.9580.0151.111
singleCellTK0.0000.0000.001
subDiffEx1.1510.0371.343
subsetSCECols0.4230.0140.492
subsetSCERows0.9870.0201.133
summarizeSCE0.1500.0090.177
trimCounts0.3640.0150.431