Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-06 11:05:05 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for debrowser on nebbiolo1


To the developers/maintainers of the debrowser package:
- Please 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 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.

raw results

Package 478/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.27.0  (landing page)
Alper Kucukural
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: master
git_last_commit: d5a7b1c
git_last_commit_date: 2022-11-01 11:13:17 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: debrowser
Version: 1.27.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings debrowser_1.27.0.tar.gz
StartedAt: 2023-02-05 20:03:26 -0500 (Sun, 05 Feb 2023)
EndedAt: 2023-02-05 20:09:21 -0500 (Sun, 05 Feb 2023)
EllapsedTime: 355.3 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings debrowser_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/debrowser.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.27.0’
* 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 ‘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 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 ... 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’
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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DEBrowser.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/debrowser.Rcheck/00check.log’
for details.



Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘debrowser’ ...
** 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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> 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 v1.27.0  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 
 11.823   0.632  12.447 

debrowser.Rcheck/tests/test-deseq.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(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 v1.27.0  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 
 28.556   1.132  29.677 

debrowser.Rcheck/tests/test-null.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> 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 v1.27.0  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 
 11.620   0.722  12.330 

debrowser.Rcheck/tests/test-ui.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> 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 v1.27.0  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 
 12.033   0.681  12.704 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0220.0040.026
IQRPlotControlsUI0.0010.0000.001
actionButtonDE0.0030.0000.003
addDataCols000
addID000
all2all0.1300.0040.133
all2allControlsUI0.0280.0000.028
applyFilters0.0010.0000.001
applyFiltersNew0.0010.0000.001
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0000.001
batchEffectUI0.0350.0000.035
batchMethod0.0020.0000.002
changeClusterOrder0.0010.0000.001
checkCountData0.0010.0000.001
checkMetaData000
clustFunParamsUI000
clusterData000
compareClust0.0010.0000.001
condSelectUI0.0290.0000.029
correctCombat000
correctHarman000
customColorsUI0.0020.0040.006
cutOffSelectionUI0.0040.0000.004
dataLCFUI0.0090.0000.009
dataLoadUI0.0080.0000.009
deServer0.0040.0040.008
deUI0.0700.0080.078
debrowserIQRplot000
debrowserall2all000
debrowserbarmainplot0.0010.0000.001
debrowserbatcheffect0.0010.0000.001
debrowserboxmainplot000
debrowsercondselect000
debrowserdataload000
debrowserdeanalysis000
debrowserdensityplot000
debrowserheatmap0.0010.0000.001
debrowserhistogram0.0010.0000.001
debrowserlowcountfilter0.0000.0010.001
debrowsermainplot0.0000.0010.001
debrowserpcaplot0.0000.0010.001
dendControlsUI0.0050.0010.005
densityPlotControlsUI0.0010.0000.001
distFunParamsUI000
drawKEGG0.0010.0000.001
drawPCAExplained000
fileTypes000
fileUploadBox0.0000.0020.002
generateTestData0.0000.0000.001
getAfterLoadMsg0.0000.0000.001
getAll2AllPlotUI0.0010.0000.001
getBSTableUI0.0010.0000.001
getBarMainPlot000
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI000
getColorShapeSelection0.0010.0000.001
getColors000
getCompSelection0.0010.0000.001
getCondMsg000
getConditionSelector000
getConditionSelectorFromMeta0.0000.0000.001
getCovariateDetails0.0010.0000.001
getCutOffSelection0.0020.0000.002
getDEAnalysisText0.0010.0000.001
getDEResultsUI0.0010.0000.001
getDataAssesmentText0.0010.0000.001
getDataForTables0.0010.0000.001
getDataPreparationText0.0010.0000.001
getDensityPlot0.0010.0000.001
getDensityPlotUI0.0010.0000.001
getDomains000
getDown000
getDownloadSection0.0060.0000.006
getEnrichDO000
getEnrichGO000
getEnrichKEGG000
getEntrezIds0.0010.0000.001
getEntrezTable000
getGOLeftMenu0.0080.0000.008
getGOPlots000
getGSEA000
getGeneList0.3050.0600.364
getGeneSetData0.0010.0000.001
getGoPanel0.0060.0040.009
getGroupSelector0.0010.0000.001
getHeatmapUI000
getHelpButton000
getHideLegendOnOff0.0010.0000.001
getHistogramUI000
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0010.0000.001
getIntroText0.0010.0000.001
getJSLine0.0010.0000.001
getKEGGModal0.0020.0000.002
getLeftMenu000
getLegendColors0.0010.0000.001
getLegendRadio0.1010.0000.101
getLegendSelect0.0020.0000.002
getLevelOrder000
getLoadingMsg0.0020.0000.002
getLogo0.0010.0000.001
getMainPanel0.0010.0000.001
getMainPlotUI000
getMainPlotsLeftMenu0.0530.0040.056
getMean000
getMergedComparison0.0000.0010.000
getMetaSelector000
getMethodDetails000
getMostVariedList000
getNormalizedMatrix0.0120.0000.013
getOrganism000
getOrganismBox0.0020.0000.002
getOrganismPathway000
getPCAPlotUI0.0010.0000.001
getPCAcontolUpdatesJS0.0010.0000.001
getPCAexplained2.6640.1082.773
getPCselection0.0000.0000.001
getPlotArea000
getProgramTitle0.0000.0000.001
getQAText0.0010.0000.002
getQCLeftMenu0.0000.0000.001
getQCPanel0.0030.0000.004
getSampleDetails0.0000.0000.001
getSampleNames000
getSamples000
getSearchData0.0010.0000.000
getSelHeat000
getSelectInputBox0.0000.0000.001
getSelectedCols000
getSelectedDatasetInput000
getShapeColor0.0010.0000.000
getStartPlotsMsg0.0030.0000.002
getStartupMsg0.0030.0000.002
getTabUpdateJS0.0000.0000.001
getTableDetails0.0000.0000.001
getTableModal0.0030.0000.004
getTableStyle0.0000.0000.001
getUp000
getUpDown000
getVariationData0.0010.0000.000
get_conditions_given_selection000
heatmapControlsUI0.0300.0060.038
heatmapJScode000
heatmapServer0.0010.0000.001
heatmapUI0.0590.0040.063
hideObj0.0000.0000.001
histogramControlsUI0.0000.0000.001
installpack000
kmeansControlsUI0.0050.0000.005
lcfMetRadio0.0020.0000.002
loadpack0.0150.0160.030
mainPlotControlsUI0.0070.0000.007
mainScatterNew0.0010.0000.001
niceKmeans0.0000.0000.001
normalizationMethods0.0020.0000.002
palUI0.0000.0020.002
panel.cor0.0000.0010.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0040.0000.004
plotData0.0000.0000.001
plotMarginsUI0.0040.0000.005
plotSizeMarginsUI0.0040.0040.008
plotSizeUI0.0000.0020.002
plotTypeUI0.0000.0010.001
plot_pca0.7860.0480.835
prepDEOutput0.0000.0000.001
prepDataContainer0.0000.0000.001
prepGroup0.0000.0000.001
prepHeatData0.0000.0000.001
prepPCADat000
push000
removeCols0.0000.0010.000
removeExtraCols0.0010.0010.002
round_vals0.0010.0000.000
runDE0.0000.0000.001
runDESeq20.0000.0000.001
runEdgeR0.0000.0010.001
runHeatmap0.0000.0010.001
runHeatmap2000
runLimma000
run_pca0.6450.0160.661
selectConditions0.0010.0000.001
selectGroupInfo0.0000.0000.001
selectedInput000
sepRadio0.0000.0020.002
setBatch0.0000.0000.001
showObj000
startDEBrowser000
startHeatmap0.0010.0000.000
textareaInput000
togglePanels0.0000.0000.001