Yichen Wang
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 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) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:45 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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. |
| Package 1856/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.6.0 (landing page) Yichen Wang
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 2022-10-19 08:07:29 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 08:29:34 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 1325.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: singleCellTK.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.2.1 (2022-06-23)
* 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 40.232 0.863 41.166
plotDoubletFinderResults 32.018 0.185 32.231
runScDblFinder 28.052 0.435 28.539
runDoubletFinder 24.459 0.066 24.582
plotTSCANPseudotimeHeatmap 23.701 0.077 23.811
importExampleData 20.472 1.985 23.210
plotBatchCorrCompare 13.965 0.152 14.123
plotMarkerDiffExp 13.566 0.052 13.637
plotScdsHybridResults 12.060 0.099 12.170
plotBcdsResults 11.123 0.161 11.300
plotDecontXResults 10.629 0.143 10.790
plotEmptyDropsResults 9.965 0.045 10.030
runEmptyDrops 9.502 0.024 9.553
plotEmptyDropsScatter 9.425 0.028 9.468
plotDEGViolin 8.701 0.068 8.794
runDecontX 8.722 0.026 8.760
plotCxdsResults 8.511 0.046 8.560
plotUMAP 7.732 0.043 7.782
findMarkerDiffExp 7.580 0.062 7.650
plotDEGRegression 7.567 0.048 7.624
detectCellOutlier 7.340 0.117 7.477
plotTSCANPseudotimeGenes 7.156 0.038 7.205
findMarkerTopTable 6.864 0.041 6.912
convertSCEToSeurat 6.273 0.211 6.492
plotDEGHeatmap 6.247 0.071 6.325
plotClusterPseudo 6.242 0.042 6.291
plotTSCANDEgenes 5.557 0.041 5.603
runSeuratSCTransform 4.996 0.125 5.136
runTSCANClusterDEAnalysis 4.995 0.027 5.028
* 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.
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)
singleCellTK.Rcheck/tests/spelling.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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
0.343 0.077 0.396
singleCellTK.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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
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**************************************************|
Calculating gene variances
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**************************************************|
Calculating feature variances of standardized and clipped values
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**************************************************|
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Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
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Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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...
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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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[ FAIL 0 | WARN 17 | SKIP 0 | PASS 162 ]
[ FAIL 0 | WARN 17 | SKIP 0 | PASS 162 ]
>
> proc.time()
user system elapsed
354.075 5.169 367.549
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| MitoGenes | 0.004 | 0.003 | 0.007 | |
| SEG | 0.005 | 0.003 | 0.007 | |
| calcEffectSizes | 0.383 | 0.008 | 0.391 | |
| combineSCE | 3.115 | 0.038 | 3.158 | |
| computeZScore | 0.479 | 0.016 | 0.496 | |
| convertSCEToSeurat | 6.273 | 0.211 | 6.492 | |
| convertSeuratToSCE | 0.852 | 0.008 | 0.862 | |
| dedupRowNames | 0.115 | 0.003 | 0.119 | |
| detectCellOutlier | 7.340 | 0.117 | 7.477 | |
| diffAbundanceFET | 0.130 | 0.003 | 0.133 | |
| discreteColorPalette | 0.011 | 0.000 | 0.010 | |
| distinctColors | 0.003 | 0.000 | 0.003 | |
| downSampleCells | 1.241 | 0.084 | 1.326 | |
| downSampleDepth | 0.988 | 0.020 | 1.009 | |
| expData-ANY-character-method | 0.603 | 0.006 | 0.610 | |
| expData-set-ANY-character-CharacterOrNullOrMissing-logical-method | 0.735 | 0.009 | 0.745 | |
| expData-set | 0.687 | 0.007 | 0.694 | |
| expData | 0.629 | 0.008 | 0.638 | |
| expDataNames-ANY-method | 0.619 | 0.005 | 0.625 | |
| expDataNames | 0.597 | 0.006 | 0.604 | |
| expDeleteDataTag | 0.060 | 0.003 | 0.063 | |
| expSetDataTag | 0.037 | 0.002 | 0.039 | |
| expTaggedData | 0.043 | 0.002 | 0.045 | |
| exportSCE | 0.040 | 0.003 | 0.043 | |
| exportSCEtoAnnData | 0.163 | 0.003 | 0.165 | |
| exportSCEtoFlatFile | 0.158 | 0.002 | 0.161 | |
| featureIndex | 0.066 | 0.004 | 0.071 | |
| findMarkerDiffExp | 7.580 | 0.062 | 7.650 | |
| findMarkerTopTable | 6.864 | 0.041 | 6.912 | |
| generateSimulatedData | 0.074 | 0.004 | 0.077 | |
| getBiomarker | 0.099 | 0.003 | 0.101 | |
| getDEGTopTable | 1.246 | 0.009 | 1.263 | |
| getDiffAbundanceResults | 0.068 | 0.001 | 0.070 | |
| getEnrichRResult | 1.532 | 0.045 | 3.302 | |
| getMSigDBTable | 0.006 | 0.002 | 0.009 | |
| getSampleSummaryStatsTable | 0.682 | 0.006 | 0.692 | |
| getSoupX | 0.807 | 0.012 | 0.819 | |
| getTSNE | 0.579 | 0.005 | 0.587 | |
| getTopHVG | 0.455 | 0.004 | 0.460 | |
| getUMAP | 4.809 | 0.034 | 4.857 | |
| importAnnData | 0.001 | 0.001 | 0.002 | |
| importBUStools | 0.531 | 0.003 | 0.535 | |
| importCellRanger | 2.205 | 0.078 | 2.300 | |
| importCellRangerV2Sample | 0.568 | 0.003 | 0.573 | |
| importCellRangerV3Sample | 0.803 | 0.014 | 0.821 | |
| importDropEst | 0.745 | 0.030 | 0.780 | |
| importExampleData | 20.472 | 1.985 | 23.210 | |
| importGeneSetsFromCollection | 1.622 | 0.109 | 1.732 | |
| importGeneSetsFromGMT | 0.118 | 0.006 | 0.125 | |
| importGeneSetsFromList | 0.247 | 0.005 | 0.252 | |
| importGeneSetsFromMSigDB | 4.493 | 0.270 | 4.768 | |
| importMitoGeneSet | 0.100 | 0.007 | 0.107 | |
| importOptimus | 0.001 | 0.001 | 0.002 | |
| importSEQC | 0.588 | 0.023 | 0.612 | |
| importSTARsolo | 0.555 | 0.003 | 0.560 | |
| iterateSimulations | 0.667 | 0.008 | 0.676 | |
| listSampleSummaryStatsTables | 0.805 | 0.008 | 0.812 | |
| mergeSCEColData | 0.984 | 0.021 | 1.008 | |
| mouseBrainSubsetSCE | 0.048 | 0.003 | 0.051 | |
| msigdb_table | 0.002 | 0.002 | 0.003 | |
| plotBarcodeRankDropsResults | 1.902 | 0.018 | 1.921 | |
| plotBarcodeRankScatter | 1.365 | 0.010 | 1.377 | |
| plotBatchCorrCompare | 13.965 | 0.152 | 14.123 | |
| plotBatchVariance | 0.527 | 0.005 | 0.533 | |
| plotBcdsResults | 11.123 | 0.161 | 11.300 | |
| plotClusterAbundance | 2.140 | 0.006 | 2.149 | |
| plotClusterPseudo | 6.242 | 0.042 | 6.291 | |
| plotCxdsResults | 8.511 | 0.046 | 8.560 | |
| plotDEGHeatmap | 6.247 | 0.071 | 6.325 | |
| plotDEGRegression | 7.567 | 0.048 | 7.624 | |
| plotDEGViolin | 8.701 | 0.068 | 8.794 | |
| plotDEGVolcano | 1.948 | 0.013 | 1.965 | |
| plotDecontXResults | 10.629 | 0.143 | 10.790 | |
| plotDimRed | 0.610 | 0.033 | 0.644 | |
| plotDoubletFinderResults | 32.018 | 0.185 | 32.231 | |
| plotEmptyDropsResults | 9.965 | 0.045 | 10.030 | |
| plotEmptyDropsScatter | 9.425 | 0.028 | 9.468 | |
| plotMASTThresholdGenes | 3.267 | 0.029 | 3.303 | |
| plotMarkerDiffExp | 13.566 | 0.052 | 13.637 | |
| plotPCA | 0.936 | 0.006 | 0.945 | |
| plotPathway | 1.588 | 0.015 | 1.608 | |
| plotRunPerCellQCResults | 0.038 | 0.003 | 0.041 | |
| plotSCEBarAssayData | 0.280 | 0.006 | 0.288 | |
| plotSCEBarColData | 0.236 | 0.003 | 0.239 | |
| plotSCEBatchFeatureMean | 0.393 | 0.004 | 0.397 | |
| plotSCEDensity | 0.489 | 0.006 | 0.496 | |
| plotSCEDensityAssayData | 0.314 | 0.003 | 0.317 | |
| plotSCEDensityColData | 0.414 | 0.005 | 0.419 | |
| plotSCEDimReduceColData | 1.555 | 0.010 | 1.568 | |
| plotSCEDimReduceFeatures | 0.713 | 0.006 | 0.720 | |
| plotSCEHeatmap | 1.456 | 0.009 | 1.468 | |
| plotSCEScatter | 0.663 | 0.006 | 0.670 | |
| plotSCEViolin | 0.427 | 0.007 | 0.438 | |
| plotSCEViolinAssayData | 0.434 | 0.007 | 0.442 | |
| plotSCEViolinColData | 0.411 | 0.006 | 0.418 | |
| plotScDblFinderResults | 40.232 | 0.863 | 41.166 | |
| plotScdsHybridResults | 12.060 | 0.099 | 12.170 | |
| plotScrubletResults | 0.038 | 0.005 | 0.044 | |
| plotSeuratElbow | 0.034 | 0.003 | 0.038 | |
| plotSeuratHVG | 0.037 | 0.003 | 0.039 | |
| plotSeuratJackStraw | 0.042 | 0.003 | 0.044 | |
| plotSeuratReduction | 0.040 | 0.004 | 0.044 | |
| plotSoupXResults | 0.344 | 0.005 | 0.349 | |
| plotTSCANDEgenes | 5.557 | 0.041 | 5.603 | |
| plotTSCANPseudotimeGenes | 7.156 | 0.038 | 7.205 | |
| plotTSCANPseudotimeHeatmap | 23.701 | 0.077 | 23.811 | |
| plotTSCANResults | 4.676 | 0.021 | 4.706 | |
| plotTSNE | 1.043 | 0.007 | 1.052 | |
| plotTopHVG | 0.932 | 0.008 | 0.942 | |
| plotUMAP | 7.732 | 0.043 | 7.782 | |
| readSingleCellMatrix | 0.007 | 0.001 | 0.008 | |
| reportCellQC | 0.382 | 0.006 | 0.389 | |
| reportDropletQC | 0.042 | 0.005 | 0.047 | |
| reportQCTool | 0.388 | 0.007 | 0.396 | |
| retrieveSCEIndex | 0.058 | 0.004 | 0.061 | |
| runBBKNN | 0 | 0 | 0 | |
| runBarcodeRankDrops | 1.055 | 0.006 | 1.062 | |
| runBcds | 3.768 | 0.059 | 3.834 | |
| runCellQC | 0.464 | 0.020 | 0.484 | |
| runComBatSeq | 0.978 | 0.012 | 0.991 | |
| runCxds | 1.073 | 0.007 | 1.081 | |
| runCxdsBcdsHybrid | 3.886 | 0.045 | 3.939 | |
| runDEAnalysis | 1.564 | 0.026 | 1.593 | |
| runDecontX | 8.722 | 0.026 | 8.760 | |
| runDimReduce | 1.969 | 0.019 | 2.004 | |
| runDoubletFinder | 24.459 | 0.066 | 24.582 | |
| runDropletQC | 0.040 | 0.005 | 0.047 | |
| runEmptyDrops | 9.502 | 0.024 | 9.553 | |
| runEnrichR | 0.458 | 0.020 | 1.658 | |
| runFastMNN | 3.478 | 0.025 | 3.514 | |
| runFeatureSelection | 0.383 | 0.001 | 0.385 | |
| runGSVA | 1.470 | 0.012 | 1.484 | |
| runKMeans | 0.812 | 0.007 | 0.820 | |
| runLimmaBC | 0.157 | 0.001 | 0.158 | |
| runMNNCorrect | 1.052 | 0.004 | 1.059 | |
| runNormalization | 1.146 | 0.007 | 1.157 | |
| runPerCellQC | 1.035 | 0.012 | 1.048 | |
| runSCANORAMA | 0.001 | 0.000 | 0.001 | |
| runSCMerge | 0.007 | 0.001 | 0.008 | |
| runScDblFinder | 28.052 | 0.435 | 28.539 | |
| runScranSNN | 0.899 | 0.011 | 0.912 | |
| runScrublet | 0.039 | 0.001 | 0.040 | |
| runSeuratFindClusters | 0.043 | 0.004 | 0.046 | |
| runSeuratFindHVG | 0.046 | 0.005 | 0.051 | |
| runSeuratHeatmap | 0.043 | 0.006 | 0.050 | |
| runSeuratICA | 0.043 | 0.004 | 0.047 | |
| runSeuratJackStraw | 0.041 | 0.005 | 0.046 | |
| runSeuratNormalizeData | 0.039 | 0.004 | 0.044 | |
| runSeuratPCA | 0.039 | 0.004 | 0.042 | |
| runSeuratSCTransform | 4.996 | 0.125 | 5.136 | |
| runSeuratScaleData | 0.043 | 0.009 | 0.052 | |
| runSeuratUMAP | 0.044 | 0.005 | 0.048 | |
| runSingleR | 0.076 | 0.003 | 0.080 | |
| runSoupX | 0.389 | 0.008 | 0.398 | |
| runTSCAN | 4.211 | 0.022 | 4.239 | |
| runTSCANClusterDEAnalysis | 4.995 | 0.027 | 5.028 | |
| runTSCANDEG | 4.093 | 0.019 | 4.117 | |
| runVAM | 1.119 | 0.009 | 1.128 | |
| runZINBWaVE | 0.007 | 0.000 | 0.007 | |
| sampleSummaryStats | 0.702 | 0.009 | 0.712 | |
| scaterCPM | 0.239 | 0.002 | 0.241 | |
| scaterPCA | 1.064 | 0.009 | 1.077 | |
| scaterlogNormCounts | 0.454 | 0.003 | 0.457 | |
| sce | 0.040 | 0.008 | 0.047 | |
| scranModelGeneVar | 0.371 | 0.003 | 0.375 | |
| sctkListGeneSetCollections | 0.352 | 0.011 | 0.363 | |
| sctkPythonInstallConda | 0 | 0 | 0 | |
| sctkPythonInstallVirtualEnv | 0 | 0 | 0 | |
| selectSCTKConda | 0 | 0 | 0 | |
| selectSCTKVirtualEnvironment | 0.000 | 0.000 | 0.001 | |
| setRowNames | 0.173 | 0.006 | 0.180 | |
| setSCTKDisplayRow | 0.749 | 0.008 | 0.760 | |
| singleCellTK | 0 | 0 | 0 | |
| subDiffEx | 0.984 | 0.025 | 1.009 | |
| subsetSCECols | 0.339 | 0.011 | 0.350 | |
| subsetSCERows | 0.853 | 0.012 | 0.865 | |
| summarizeSCE | 0.110 | 0.003 | 0.113 | |
| trimCounts | 0.440 | 0.006 | 0.447 | |