Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-12 12:05 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 521/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.37.0  (landing page)
Alper Kucukural
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: devel
git_last_commit: ab3c2a8
git_last_commit_date: 2025-04-15 10:59:48 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for debrowser on nebbiolo2

To the developers/maintainers of the debrowser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/debrowser.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: debrowser
Version: 1.37.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings debrowser_1.37.0.tar.gz
StartedAt: 2025-08-12 00:24:22 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 00:31:21 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 419.4 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings debrowser_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/debrowser.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.37.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘debrowser’ can be installed ... OK
* checking installed package size ... OK
* 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 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 ... NOTE
checkCountData : <anonymous>: no visible binding for global variable
  ‘err’
debrowserdataload: no visible binding for global variable ‘demodata’
debrowserhistogram: no visible global function definition for ‘config’
generateTestData: no visible binding for global variable ‘metadata’
getBarMainPlot: no visible global function definition for ‘config’
getBoxMainPlot: no visible global function definition for ‘config’
getDensityPlot: no visible binding for global variable ‘samples’
getDensityPlot: no visible global function definition for ‘config’
getGOPlots: no visible global function definition for ‘facet_grid’
getGSEA: no visible global function definition for ‘is’
getIQRPlot: no visible global function definition for ‘config’
mainScatterNew: no visible global function definition for ‘config’
plot_pca: no visible binding for global variable ‘x’
plot_pca: no visible binding for global variable ‘y’
plot_pca: no visible binding for global variable ‘textName’
plot_pca: no visible global function definition for ‘config’
runHeatmap: no visible global function definition for ‘config’
Undefined global functions or variables:
  config demodata err facet_grid is metadata samples textName x y
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-demo.R’
  Running ‘test-deseq.R’
  Running ‘test-null.R’
  Running ‘test-ui.R’
 OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/debrowser.Rcheck/00check.log’
for details.


Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘debrowser’ ...
** this is package ‘debrowser’ version ‘1.37.0’
** using staged installation
** R
** 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 (debrowser)

Tests output

debrowser.Rcheck/tests/test-demo.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.37.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("demo data can be loaded", {
+     load(system.file("extdata", "demo", "demodata.Rda",
+         package = "debrowser"))
+     expect_true(is.data.frame(demodata))
+     expect_equal(demodata[29311, 2], 2)
+     expect_equal(demodata[29311, 5], 7.1)
+     expect_equal(demodata[29311, 6], 6)
+     expect_null(demodata[1, 7])
+ })
Test passed 😀
> 
> proc.time()
   user  system elapsed 
 14.318   0.861  15.168 

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.37.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> load(system.file("extdata", "demo", "demodata.Rda",
+     package = "debrowser"))
> metadata <- metadatatable 
> columns <- c("exper_rep1", "exper_rep2", "exper_rep3",
+     "control_rep1", "control_rep2", "control_rep3")
> conds <- factor( c("Control", "Control", "Control",
+     "Treat", "Treat", "Treat") )
> data <- data.frame(demodata[, columns])
> 
> #Run DESeq2 with the following parameters
> params <- c("DESeq2", "NoCovariate", "parametric", F, "Wald", "None") 
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+     deseqrun <- runDE(data, metadata, columns, conds, params)
+     expect_true(exists("deseqrun"))
+ })
Test passed 😸
> 
> ##################################################
> deseqrun <- runDE(data, metadata, columns, conds, params)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> 
> de_res <- data.frame(deseqrun)
> norm_data <- getNormalizedMatrix(data[, columns])
> rdata <- cbind(rownames(de_res), norm_data[rownames(de_res), columns],
+                 log10(rowMeans(norm_data[rownames(de_res),
+                 paste(c("exper_rep1", "exper_rep2", "exper_rep3"))])
+                 + 0.1), log10( rowMeans( norm_data[ rownames( de_res ),
+                 paste(c("control_rep1", "control_rep2", "control_rep3"))])
+                 + 0.1), de_res[rownames(de_res),
+                 c("padj", "log2FoldChange")], 2 ^ de_res[rownames(de_res),
+                 "log2FoldChange"], -1 *
+                 log10(de_res[rownames(de_res), "padj"]))
> colnames(rdata) <- c("ID", columns, "Cond1", "Cond2", "padj",
+                 "log2FoldChange", "foldChange", "log10padj")
> rdata <- as.data.frame(rdata)
> rdata$padj[is.na(rdata$padj)] <- 1
> 
> padj_cutoff <- 0.01
> foldChange_cutoff <- 2
> 
> rdata$Legend <- character(nrow(rdata))
> rdata$Legend[rdata$log2FoldChange > log2(foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Up"
> rdata$Legend[rdata$log2FoldChange < log2(1 / foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Down"
> rdata$Legend[abs(rdata$log2FoldChange) <= 
+         log2(foldChange_cutoff)] <- "NS"
> rdata$Legend[is.null(rdata$log10padj)] <- "NA"
> rdata$Size <- character(nrow(rdata))
> rdata[, "Size"] <- "40"
> 
> dat <- rdata
> dat$M <- rdata$Cond1 - rdata$Cond2
> dat$A <- (rdata$Cond1 + rdata$Cond2) / 2
> 
> updown <- rdata[rdata$Legend=="Up" | rdata$Legend=="Down",columns]
> ##################################################
> 
> 
> 
> proc.time()
   user  system elapsed 
 32.309   0.754  33.040 

debrowser.Rcheck/tests/test-null.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.37.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("passing no data returns NULL", {
+     expect_null(compareClust() )
+     expect_null(getGOPlots(NULL, NULL))
+     null_deseq <- runDE(NULL)
+     expect_null(null_deseq)
+     expect_null(plot_pca(NULL))
+ })
Test passed 😀
> 
> proc.time()
   user  system elapsed 
 12.965   0.850  13.804 

debrowser.Rcheck/tests/test-ui.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> require(shiny)
Loading required package: shiny
> library(debrowser)



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
DEBrowser v1.37.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("able to create panel UI", {
+     expect_silent( QCPanel <- getQCPanel() )
+     expect_true(exists("QCPanel"))
+     expect_equal(QCPanel[[1]][[1]], "div")
+ 
+     expect_silent( downloads <- getDownloadSection() )
+     expect_true(exists("downloads"))
+     expect_equal(downloads[[1]][[1]], "div")
+ 
+     expect_silent( getMain <- getMainPanel() )
+     expect_true(exists("getMain"))
+     expect_equal(getMain[[1]][[1]], "div")
+ 
+     expect_silent( getStart <- getStartupMsg() )
+     expect_true(exists("getStart"))
+     expect_equal(getStart[[1]][[1]], "div")
+ 
+     expect_silent( getAfter <- getAfterLoadMsg() )
+     expect_true(exists("getAfter"))
+     expect_equal(getAfter[[1]][[1]], "div")
+ 
+     expect_silent(getGO <- getGoPanel() )
+     expect_true(exists("getGO"))
+     expect_equal(getGO[[1]][[1]], "div")
+ })
Test passed 🌈
> 
> proc.time()
   user  system elapsed 
 13.101   0.875  13.964 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0220.0000.022
IQRPlotControlsUI0.0010.0000.002
actionButtonDE0.0030.0010.003
addDataCols000
addID000
all2all0.1280.0090.137
all2allControlsUI0.0300.0010.031
applyFilters0.0000.0000.001
applyFiltersNew0.0010.0000.000
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0000.002
batchEffectUI0.0390.0060.045
batchMethod0.0010.0010.002
changeClusterOrder0.0010.0000.000
checkCountData0.0000.0010.000
checkMetaData000
clustFunParamsUI000
clusterData000
compareClust0.0010.0000.001
condSelectUI0.0050.0000.005
correctCombat0.0010.0000.000
correctHarman000
customColorsUI0.0030.0010.005
cutOffSelectionUI0.0030.0000.004
dataLCFUI0.0110.0000.011
dataLoadUI0.010.000.01
deServer0.0040.0010.005
deUI0.0880.0130.101
debrowserIQRplot000
debrowserall2all0.0000.0000.001
debrowserbarmainplot000
debrowserbatcheffect0.0000.0000.001
debrowserboxmainplot0.0010.0000.000
debrowsercondselect000
debrowserdataload0.0000.0000.001
debrowserdeanalysis0.0000.0000.001
debrowserdensityplot000
debrowserheatmap0.0000.0000.001
debrowserhistogram0.0000.0000.001
debrowserlowcountfilter000
debrowsermainplot0.0000.0010.000
debrowserpcaplot0.0000.0000.001
dendControlsUI0.0050.0010.006
densityPlotControlsUI0.0000.0010.001
distFunParamsUI000
drawKEGG0.0000.0010.000
drawPCAExplained000
fileTypes000
fileUploadBox0.0030.0000.002
generateTestData000
getAfterLoadMsg000
getAll2AllPlotUI0.0000.0000.001
getBSTableUI000
getBarMainPlot000
getBarMainPlotUI0.0000.0000.001
getBoxMainPlot000
getBoxMainPlotUI000
getColorShapeSelection0.0000.0000.001
getColors000
getCompSelection0.0010.0010.002
getCondMsg000
getConditionSelector000
getConditionSelectorFromMeta0.0010.0000.000
getCovariateDetails000
getCutOffSelection0.0030.0000.003
getDEAnalysisText0.0010.0000.002
getDEResultsUI0.0010.0000.001
getDataAssesmentText0.0000.0010.002
getDataForTables0.0000.0000.001
getDataPreparationText0.0010.0000.001
getDensityPlot0.0010.0000.001
getDensityPlotUI000
getDomains000
getDown000
getDownloadSection0.0060.0020.008
getEnrichDO000
getEnrichGO000
getEnrichKEGG0.0000.0000.001
getEntrezIds000
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0090.0010.010
getGOPlots0.0010.0000.000
getGSEA000
getGeneList0.6860.0470.733
getGeneSetData0.0010.0000.000
getGoPanel0.0110.0010.012
getGroupSelector0.0000.0010.000
getHeatmapUI000
getHelpButton0.0010.0000.000
getHideLegendOnOff0.0010.0000.001
getHistogramUI000
getIQRPlot0.0010.0000.001
getIQRPlotUI000
getIntroText0.0010.0000.001
getJSLine0.0020.0000.002
getKEGGModal0.0030.0000.002
getLeftMenu000
getLegendColors0.0010.0000.001
getLegendRadio0.0020.0000.002
getLegendSelect0.0020.0000.002
getLevelOrder0.0000.0000.001
getLoadingMsg0.0020.0000.002
getLogo0.0000.0010.001
getMainPanel0.0000.0000.001
getMainPlotUI000
getMainPlotsLeftMenu0.0620.0010.063
getMean0.0000.0000.001
getMergedComparison000
getMetaSelector000
getMethodDetails0.0010.0000.001
getMostVariedList000
getNormalizedMatrix0.0120.0010.013
getOrganism0.0000.0000.001
getOrganismBox0.0020.0000.002
getOrganismPathway0.0000.0000.001
getPCAPlotUI000
getPCAcontolUpdatesJS000
getPCAexplained1.9970.0902.087
getPCselection0.0010.0000.000
getPlotArea000
getProgramTitle0.0000.0000.001
getQAText0.0010.0000.001
getQCLeftMenu000
getQCPanel0.0020.0000.002
getSampleDetails000
getSampleNames0.0010.0000.000
getSearchData000
getSelHeat0.0000.0000.001
getSelectInputBox000
getSelectedCols0.0000.0000.001
getSelectedDatasetInput000
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0020.0000.002
getStartupMsg0.0020.0000.002
getTabUpdateJS0.0000.0000.001
getTableDetails000
getTableModal0.0020.0000.003
getTableStyle000
getUp0.0010.0000.000
getUpDown000
getVariationData000
get_conditions_given_selection000
heatmapControlsUI0.0300.0000.031
heatmapJScode000
heatmapServer0.0010.0000.001
heatmapUI0.0530.0010.055
hideObj000
histogramControlsUI000
installpack000
kmeansControlsUI0.0040.0000.005
lcfMetRadio0.0010.0000.002
loadpack0.0010.0010.002
mainPlotControlsUI0.0030.0010.004
mainScatterNew0.0010.0000.001
niceKmeans0.0000.0000.001
normalizationMethods0.0010.0000.001
palUI0.0010.0000.001
panel.cor000
panel.hist0.0000.0000.001
pcaPlotControlsUI0.0040.0000.004
plotData000
plotMarginsUI0.0040.0000.004
plotSizeMarginsUI0.0070.0000.007
plotSizeUI0.0020.0000.002
plotTypeUI000
plot_pca0.7790.0380.817
prepDataContainer0.0010.0000.000
prepGroup0.0010.0000.000
prepHeatData000
prepPCADat0.0010.0000.000
push000
removeCols000
removeExtraCols0.0010.0000.001
round_vals000
runDE000
runDESeq20.0010.0000.000
runEdgeR0.0010.0000.001
runHeatmap0.0000.0000.001
runHeatmap2000
runLimma0.0010.0000.000
run_pca1.5830.0351.619
selectConditions0.0010.0000.001
selectGroupInfo0.0010.0000.000
selectedInput000
sepRadio0.0020.0000.002
setBatch000
showObj000
startDEBrowser000
startHeatmap000
textareaInput000
togglePanels0.0010.0000.000