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This page was generated on 2024-09-12 11:41 -0400 (Thu, 12 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4713
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4450
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4483
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4430
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4428
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 1953/2258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.15.0  (landing page)
Joshua David Campbell
Snapshot Date: 2024-09-11 14:00 -0400 (Wed, 11 Sep 2024)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: devel
git_last_commit: 4d7a515
git_last_commit_date: 2024-04-30 11:06:02 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for singleCellTK on nebbiolo2

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: 2.15.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings singleCellTK_2.15.0.tar.gz
StartedAt: 2024-09-12 03:13:14 -0400 (Thu, 12 Sep 2024)
EndedAt: 2024-09-12 03:27:07 -0400 (Thu, 12 Sep 2024)
EllapsedTime: 833.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: singleCellTK.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings singleCellTK_2.15.0.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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.15.0’
* 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:
    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 ... 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 ... ERROR
Running examples in ‘singleCellTK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runGSVA
> ### Title: Run GSVA analysis on a SingleCellExperiment object
> ### Aliases: runGSVA
> 
> ### ** Examples
> 
> data(scExample, package = "singleCellTK")
> sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
> sce <- scaterlogNormCounts(sce, assayName = "logcounts")
> gs1 <- rownames(sce)[seq(10)]
> gs2 <- rownames(sce)[seq(11,20)]
> gs <- list("geneset1" = gs1, "geneset2" = gs2)
> 
> sce <- importGeneSetsFromList(inSCE = sce,geneSetList = gs,
+                                            by = "rownames")
> sce <- runGSVA(inSCE = sce, 
+                geneSetCollectionName = "GeneSetCollection", 
+                useAssay = "logcounts")
Thu Sep 12 03:22:13 2024 ... Running GSVA
ℹ GSVA version 1.53.20
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': No identifiers in the gene sets could be matched to the identifiers in the expression data.
Calls: runGSVA ... .filterAndMapGenesAndGeneSets -> .mapGeneSetsToFeatures
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─singleCellTK::runGSVA(...) at test-pathway.R:36:5
    2. │ ├─base::t(GSVA::gsva(gsvaPar))
    3. │ ├─GSVA::gsva(gsvaPar)
    4. │ └─GSVA::gsva(gsvaPar)
    5. │   └─GSVA (local) .local(param, ...)
    6. │     └─GSVA:::.filterAndMapGenesAndGeneSets(...)
    7. │       └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
    8. │         └─base::stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")
    9. └─base::.handleSimpleError(...)
   10.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 20 | SKIP 0 | PASS 221 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 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/bbs-3.20-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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: x86_64-pc-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 
  0.169   0.022   0.180

singleCellTK.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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, 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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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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

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Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 2 | WARN 20 | SKIP 0 | PASS 221 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-misc.R:64:3'): Testing runGSVA ─────────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 't': No identifiers in the gene sets could be matched to the identifiers in the expression data.
Backtrace:
     ▆
  1. ├─singleCellTK::runGSVA(...) at test-misc.R:64:3
  2. │ ├─base::t(GSVA::gsva(gsvaPar))
  3. │ ├─GSVA::gsva(gsvaPar)
  4. │ └─GSVA::gsva(gsvaPar)
  5. │   └─GSVA (local) .local(param, ...)
  6. │     └─GSVA:::.filterAndMapGenesAndGeneSets(...)
  7. │       └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
  8. │         └─base::stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))
── Error ('test-pathway.R:36:5'): Testing GSVA ─────────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 't': No identifiers in the gene sets could be matched to the identifiers in the expression data.
Backtrace:
     ▆
  1. ├─singleCellTK::runGSVA(...) at test-pathway.R:36:5
  2. │ ├─base::t(GSVA::gsva(gsvaPar))
  3. │ ├─GSVA::gsva(gsvaPar)
  4. │ └─GSVA::gsva(gsvaPar)
  5. │   └─GSVA (local) .local(param, ...)
  6. │     └─GSVA:::.filterAndMapGenesAndGeneSets(...)
  7. │       └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
  8. │         └─base::stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))

[ FAIL 2 | WARN 20 | SKIP 0 | PASS 221 ]
Error: Test failures
Execution halted

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0020.0000.003
SEG0.0020.0000.003
calcEffectSizes0.1540.0000.155
combineSCE2.0330.0602.094
computeZScore0.2310.0040.236
convertSCEToSeurat3.3680.1363.505
convertSeuratToSCE1.4290.0281.457
dedupRowNames0.0540.0000.054
detectCellOutlier5.0160.1925.208
diffAbundanceFET0.0580.0000.057
discreteColorPalette0.0070.0000.006
distinctColors0.0020.0000.002
downSampleCells0.5960.0600.655
downSampleDepth0.4620.0120.475
expData-ANY-character-method0.2690.0000.270
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.3130.0120.325
expData-set0.3170.0000.317
expData0.2830.0200.302
expDataNames-ANY-method0.2780.0040.282
expDataNames0.2540.0030.257
expDeleteDataTag0.0330.0000.034
expSetDataTag0.0240.0000.024
expTaggedData0.0250.0000.026
exportSCE0.0220.0000.022
exportSCEtoAnnData0.0920.0030.096
exportSCEtoFlatFile0.0970.0000.096
featureIndex0.0360.0000.035
generateSimulatedData0.050.000.05
getBiomarker0.0550.0000.055
getDEGTopTable0.8010.0200.822
getDiffAbundanceResults0.0430.0040.047
getEnrichRResult0.4220.0075.973
getFindMarkerTopTable3.1950.1123.308
getMSigDBTable0.0040.0000.003
getPathwayResultNames0.0240.0000.023
getSampleSummaryStatsTable0.2940.0040.299
getSoupX000
getTSCANResults1.6360.0321.668
getTopHVG1.1400.0161.156
importAnnData0.0010.0000.002
importBUStools0.2320.0160.249
importCellRanger0.9190.0040.923
importCellRangerV2Sample0.2280.0000.228
importCellRangerV3Sample0.3520.0040.355
importDropEst0.2740.0000.274
importExampleData17.850 1.56719.938
importGeneSetsFromCollection0.7750.0110.787
importGeneSetsFromGMT0.0680.0000.068
importGeneSetsFromList0.1200.0050.124
importGeneSetsFromMSigDB2.3800.0992.480
importMitoGeneSet0.0520.0000.053
importOptimus0.0020.0000.002
importSEQC0.2350.0000.236
importSTARsolo0.2480.0000.248
iterateSimulations0.3780.0000.378
listSampleSummaryStatsTables0.3790.0030.384
mergeSCEColData0.4510.0160.467
mouseBrainSubsetSCE0.0390.0000.040
msigdb_table0.0020.0000.001
plotBarcodeRankDropsResults1.0140.0011.013
plotBarcodeRankScatter0.9460.0030.949
plotBatchCorrCompare10.427 0.19610.616
plotBatchVariance0.3080.0280.335
plotBcdsResults7.8920.1567.146
plotBubble0.9500.0320.982
plotClusterAbundance0.7610.0000.761
plotCxdsResults5.9540.1336.084
plotDEGHeatmap2.6910.0402.731
plotDEGRegression3.4440.0083.445
plotDEGViolin4.0580.1044.156
plotDEGVolcano0.9250.0120.936
plotDecontXResults7.2690.1447.413
plotDimRed0.2780.0000.277
plotDoubletFinderResults31.201 0.30031.497
plotEmptyDropsResults6.7140.0246.739
plotEmptyDropsScatter6.6740.0446.717
plotFindMarkerHeatmap4.110.044.15
plotMASTThresholdGenes1.5010.0351.537
plotPCA0.5030.0080.512
plotPathway0.7480.0040.752
plotRunPerCellQCResults2.0730.0002.073
plotSCEBarAssayData0.2100.0040.214
plotSCEBarColData0.1350.0000.135
plotSCEBatchFeatureMean0.1970.0000.197
plotSCEDensity0.1980.0080.206
plotSCEDensityAssayData0.1570.0080.165
plotSCEDensityColData0.1970.0000.197
plotSCEDimReduceColData0.7640.0000.764
plotSCEDimReduceFeatures0.3680.0080.376
plotSCEHeatmap0.6490.0120.661
plotSCEScatter0.3480.0120.360
plotSCEViolin0.2360.0120.248
plotSCEViolinAssayData0.2810.0120.292
plotSCEViolinColData0.2360.0080.244
plotScDblFinderResults28.467 0.38028.845
plotScanpyDotPlot0.0260.0000.025
plotScanpyEmbedding0.0260.0000.026
plotScanpyHVG0.0250.0000.026
plotScanpyHeatmap0.0260.0000.026
plotScanpyMarkerGenes0.0270.0000.027
plotScanpyMarkerGenesDotPlot0.0260.0000.026
plotScanpyMarkerGenesHeatmap0.0250.0000.025
plotScanpyMarkerGenesMatrixPlot0.0210.0040.025
plotScanpyMarkerGenesViolin0.0270.0000.027
plotScanpyMatrixPlot0.0260.0000.026
plotScanpyPCA0.0250.0000.025
plotScanpyPCAGeneRanking0.0260.0000.026
plotScanpyPCAVariance0.0250.0000.025
plotScanpyViolin0.0240.0000.024
plotScdsHybridResults10.128 0.204 9.399
plotScrubletResults0.0250.0000.025
plotSeuratElbow0.0230.0000.024
plotSeuratHVG0.0240.0000.024
plotSeuratJackStraw0.0230.0000.024
plotSeuratReduction0.0240.0000.023
plotSoupXResults000
plotTSCANClusterDEG5.1160.0125.129
plotTSCANClusterPseudo2.1150.0002.116
plotTSCANDimReduceFeatures2.0980.0162.115
plotTSCANPseudotimeGenes1.9310.0081.939
plotTSCANPseudotimeHeatmap2.1950.0082.202
plotTSCANResults2.0060.0122.017
plotTSNE0.4570.0040.460
plotTopHVG0.5220.0080.530
plotUMAP6.3840.1006.481
readSingleCellMatrix0.0050.0000.005
reportCellQC0.1610.0000.161
reportDropletQC0.0230.0000.024
reportQCTool0.1630.0000.163
retrieveSCEIndex0.0290.0000.029
runBBKNN000
runBarcodeRankDrops0.3850.0000.385
runBcds2.2840.0481.449
runCellQC0.1660.0000.165
runClusterSummaryMetrics0.6360.0000.636
runComBatSeq0.4320.0000.431
runCxds0.4770.0040.482
runCxdsBcdsHybrid2.3810.0161.478
runDEAnalysis0.6770.0000.678
runDecontX6.9260.0116.937
runDimReduce0.4360.0000.436
runDoubletFinder30.286 0.16030.446
runDropletQC0.0210.0040.024
runEmptyDrops6.4910.0086.498
runEnrichR0.4770.0481.805
runFastMNN1.6870.0241.711
runFeatureSelection0.2130.0000.213
runFindMarker3.3620.2283.591