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CHECK report for debrowser on celaya2

This page was generated on 2019-10-16 12:57:31 -0400 (Wed, 16 Oct 2019).

Package 396/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.12.3
Alper Kucukural
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/debrowser
Branch: RELEASE_3_9
Last Commit: a21fc72
Last Changed Date: 2019-08-09 16:02:14 -0400 (Fri, 09 Aug 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: debrowser
Version: 1.12.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings debrowser_1.12.3.tar.gz
StartedAt: 2019-10-16 02:00:26 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:09:48 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 562.1 seconds
RetCode: 0
Status:  OK 
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings debrowser_1.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/debrowser.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.12.3’
* 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 : : 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’
getIQRPlot: no visible global function definition for ‘config’
getMean: no visible binding for global variable ‘norm_data’
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 ‘samples’
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 norm_data samples x y
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/debrowser.Rcheck/00check.log’
for details.

Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> 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 v1.12.3  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])
+ })
> 
> proc.time()
   user  system elapsed 
 18.922   1.893  20.768

debrowser.Rcheck/tests/test-deseq.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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 v1.12.3  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"))
> 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])
> params <-
+         #Run DESeq2 with the following parameters
+         c("DESeq2", "parametric", F, "Wald") 
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+     deseqrun <- runDE(data, columns, conds, params)
+     expect_true(exists("deseqrun"))
+ })
> 
> ##################################################
> deseqrun <- runDE(data, 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]
> ##################################################
> 
> test_that("Check the QC plots", {
+     expect_silent( all2all(data) )
+ })
> 
> 
> proc.time()
   user  system elapsed 
 51.270   3.108  54.338

debrowser.Rcheck/tests/test-null.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> 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 v1.12.3  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))
+ })
> 
> proc.time()
   user  system elapsed 
 19.496   1.996  21.458

debrowser.Rcheck/tests/test-ui.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> 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 v1.12.3  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")
+ })
> 
> proc.time()
   user  system elapsed 
 19.066   2.050  21.068

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0100.0000.011
IQRPlotControlsUI0.0010.0000.001
actionButtonDE0.0070.0010.007
addDataCols0.0010.0000.001
addID0.0000.0000.001
all2all0.2190.0030.223
all2allControlsUI0.0030.0010.003
applyFilters0.0010.0000.000
applyFiltersNew0.0010.0010.000
applyFiltersToMergedComparison0.0000.0000.001
barMainPlotControlsUI0.0010.0010.002
batchEffectUI0.0920.0070.100
batchMethod0.0050.0000.005
changeClusterOrder0.0010.0010.001
checkCountData0.0010.0010.001
checkMetaData000
clustFunParamsUI0.0000.0000.001
clusterData0.0010.0000.000
compareClust0.0000.0000.001
condSelectUI0.0070.0000.007
correctCombat0.0010.0000.001
correctHarman0.0000.0000.001
customColorsUI0.0120.0030.016
cutOffSelectionUI0.0060.0000.007
dataLCFUI0.0440.0050.049
dataLoadUI0.0350.0030.038
deServer0.0200.0040.024
deUI1.3600.2151.678
debrowserIQRplot0.0010.0010.001
debrowserall2all0.0010.0000.001
debrowserbarmainplot0.0010.0000.001
debrowserbatcheffect0.0010.0000.002
debrowserboxmainplot0.0010.0000.001
debrowsercondselect0.0010.0000.001
debrowserdataload0.0010.0000.001
debrowserdeanalysis0.0010.0000.001
debrowserdensityplot0.0010.0000.001
debrowserheatmap0.0010.0000.001
debrowserhistogram0.0010.0000.001
debrowserlowcountfilter0.0010.0000.001
debrowsermainplot0.0010.0000.001
debrowserpcaplot0.0010.0010.001
dendControlsUI0.0170.0030.021
densityPlotControlsUI0.0030.0010.004
distFunParamsUI0.0000.0000.001
drawKEGG0.0000.0000.001
drawPCAExplained0.0000.0000.001
fileTypes0.0000.0000.001
fileUploadBox0.0080.0000.008
generateTestData0.0010.0000.001
getAfterLoadMsg0.0010.0000.001
getAll2AllPlotUI0.0000.0000.001
getBSTableUI0.0000.0000.001
getBarMainPlot0.0010.0010.001
getBarMainPlotUI0.0010.0010.001
getBoxMainPlot0.0010.0000.001
getBoxMainPlotUI0.0010.0000.001
getColorShapeSelection0.0010.0010.000
getColors0.0010.0000.001
getCompSelection0.0040.0000.004
getCondMsg0.0010.0000.001
getConditionSelector0.0000.0010.001
getConditionSelectorFromMeta0.0040.0000.005
getCutOffSelection0.0030.0000.003
getDEAnalysisText0.0040.0000.005
getDEResultsUI0.0020.0010.002
getDataAssesmentText0.0030.0000.004
getDataForTables0.0000.0000.001
getDataPreparationText0.0020.0000.003
getDensityPlot0.0000.0010.001
getDensityPlotUI0.0000.0000.001
getDomains000
getDown0.0000.0000.001
getDownloadSection0.0180.0010.019
getEnrichDO0.0000.0000.001
getEnrichGO0.0000.0010.001
getEnrichKEGG0.0000.0010.001
getEntrezIds0.0010.0000.001
getEntrezTable0.0010.0000.001
getGOLeftMenu0.0220.0000.023
getGOPlots0.0000.0000.001
getGeneList1.9240.1232.047
getGeneSetData0.0000.0000.001
getGoPanel0.0420.0050.048
getHeatmapUI0.0000.0000.001
getHelpButton0.0000.0010.000
getHideLegendOnOff0.0040.0000.005
getHistogramUI0.0000.0000.001
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0010.0010.001
getIntroText0.0030.0000.003
getJSLine0.0110.0010.013
getKEGGModal0.0040.0000.005
getLeftMenu0.0000.0010.001
getLegendColors0.0010.0000.001
getLegendRadio0.0040.0000.004
getLegendSelect0.0050.0000.005
getLevelOrder0.0010.0000.000
getLoadingMsg0.0030.0010.005
getLogo0.0020.0010.002
getMainPanel0.0020.0000.002
getMainPlotUI0.0010.0000.001
getMainPlotsLeftMenu0.0980.0020.100
getMean000
getMergedComparison0.0000.0000.001
getMetaSelector0.0010.0000.001
getMethodDetails0.0000.0000.001
getMostVariedList000
getNormalizedMatrix0.0190.0010.020
getOrganism0.0000.0000.001
getOrganismBox0.0040.0010.005
getOrganismPathway0.0000.0000.001
getPCAPlotUI0.0010.0000.001
getPCAcontolUpdatesJS0.0010.0010.000
getPCAexplained2.8520.3703.224
getPCselection0.0010.0010.001
getPlotArea0.0000.0010.001
getProgramTitle0.0010.0000.001
getQAText0.0020.0000.002
getQCLeftMenu0.0000.0010.001
getQCPanel0.0040.0000.004
getSampleDetails0.0010.0000.000
getSampleNames0.0010.0000.001
getSamples0.0000.0010.000
getSearchData0.0000.0000.001
getSelHeat0.0000.0000.001
getSelectInputBox0.0010.0000.000
getSelectedCols0.0010.0010.001
getSelectedDatasetInput0.0010.0000.000
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0040.0010.004
getStartupMsg0.0050.0010.005
getTabUpdateJS0.0000.0010.001
getTableDetails0.0000.0000.001
getTableModal0.0170.0020.019
getTableStyle0.0010.0000.001
getTextOnOff0.0060.0000.005
getUp0.0010.0000.000
getUpDown000
getVariationData0.0000.0000.001
get_conditions_given_selection0.0000.0000.001
heatmapControlsUI0.0690.0020.070
heatmapJScode0.0000.0000.001
heatmapServer0.0030.0000.003
heatmapUI0.1420.0080.150
hideObj0.0000.0000.001
histogramControlsUI0.0010.0000.001
installpack0.0010.0000.001
kmeansControlsUI0.010.000.01
lcfMetRadio0.0030.0000.002
loadpack0.0170.0280.045
mainPlotControlsUI0.0080.0000.008
mainScatterNew0.0010.0000.001
niceKmeans0.0010.0000.001
normalizationMethods0.0020.0010.003
palUI0.0030.0000.003
panel.cor0.0010.0000.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0130.0010.013
plotData0.0010.0010.001
plotMarginsUI0.0060.0000.006
plotSizeMarginsUI0.0130.0000.014
plotSizeUI0.0050.0000.004
plotTypeUI0.0020.0000.002
plot_pca1.3620.1291.490
prepDEOutput000
prepDataContainer0.0000.0000.001
prepGroup0.0010.0000.001
prepHeatData0.0010.0000.000
prepPCADat0.0010.0000.001
push0.0010.0010.000
removeCols0.0000.0000.001
removeExtraCols0.0010.0010.002
round_vals0.0010.0000.000
runDE0.0010.0000.001
runDESeq20.0010.0000.001
runEdgeR000
runHeatmap0.0010.0000.001
runHeatmap20.0000.0000.001
runLimma0.0000.0000.001
run_pca2.0020.1702.203
selectConditions0.0010.0000.001
selectGroupInfo0.0010.0000.000
selectedInput0.0000.0000.001
sepRadio0.0030.0000.004
setBatch0.0010.0000.000
showObj0.0010.0000.001
startDEBrowser0.0010.0010.001
startHeatmap0.0010.0010.001
textareaInput0.0010.0000.001
togglePanels0.0010.0000.000