Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:49 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for debrowser on merida1


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 479/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.24.1  (landing page)
Alper Kucukural
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_15
git_last_commit: c03e0a0
git_last_commit_date: 2022-08-01 13:53:14 -0400 (Mon, 01 Aug 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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: 1.24.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings debrowser_1.24.1.tar.gz
StartedAt: 2022-10-19 01:19:50 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:29:57 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 607.3 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings debrowser_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/debrowser.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.24.1’
* 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’
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 samples textName 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-3.15-bioc/meat/debrowser.Rcheck/00check.log’
for details.

Installation output

debrowser.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 v1.24.1  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 
 24.218   1.152  25.608

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(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 v1.24.1  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 
 63.137   1.629  65.233

debrowser.Rcheck/tests/test-null.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 v1.24.1  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 
 23.341   1.129  24.522

debrowser.Rcheck/tests/test-ui.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 v1.24.1  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 
 23.448   1.149  24.703

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0370.0040.041
IQRPlotControlsUI0.0020.0000.002
actionButtonDE0.0070.0000.008
addDataCols0.0010.0010.000
addID000
all2all0.3180.0090.327
all2allControlsUI0.0490.0040.054
applyFilters0.0010.0000.001
applyFiltersNew0.0010.0010.000
applyFiltersToMergedComparison0.0000.0000.001
barMainPlotControlsUI0.0020.0010.003
batchEffectUI0.0770.0060.084
batchMethod0.0030.0000.003
changeClusterOrder0.0010.0010.000
checkCountData0.0000.0000.001
checkMetaData0.0000.0010.001
clustFunParamsUI0.0010.0000.001
clusterData0.0000.0010.001
compareClust000
condSelectUI0.0070.0010.007
correctCombat0.0010.0000.001
correctHarman0.0000.0000.001
customColorsUI0.0110.0020.014
cutOffSelectionUI0.0070.0000.007
dataLCFUI0.0330.0030.036
dataLoadUI0.0280.0020.029
deServer0.0130.0030.015
deUI0.2200.0130.233
debrowserIQRplot0.0010.0010.001
debrowserall2all000
debrowserbarmainplot000
debrowserbatcheffect0.0010.0000.001
debrowserboxmainplot0.0000.0010.001
debrowsercondselect000
debrowserdataload0.0010.0010.002
debrowserdeanalysis0.0010.0000.001
debrowserdensityplot0.0000.0010.001
debrowserheatmap0.0010.0000.001
debrowserhistogram0.0000.0010.001
debrowserlowcountfilter0.0010.0000.001
debrowsermainplot0.0010.0000.001
debrowserpcaplot0.0000.0000.001
dendControlsUI0.0110.0000.012
densityPlotControlsUI0.0020.0000.002
distFunParamsUI000
drawKEGG0.0000.0000.001
drawPCAExplained000
fileTypes0.0000.0000.001
fileUploadBox0.0060.0010.006
generateTestData0.0010.0000.001
getAfterLoadMsg0.0010.0000.001
getAll2AllPlotUI0.0010.0000.001
getBSTableUI0.0010.0000.000
getBarMainPlot0.0000.0000.001
getBarMainPlotUI0.0000.0000.001
getBoxMainPlot0.0010.0000.001
getBoxMainPlotUI0.0010.0000.000
getColorShapeSelection0.0000.0010.001
getColors000
getCompSelection0.0020.0000.003
getCondMsg0.0010.0000.001
getConditionSelector000
getConditionSelectorFromMeta0.0000.0010.001
getCovariateDetails0.0000.0000.001
getCutOffSelection0.0030.0010.003
getDEAnalysisText0.0030.0000.003
getDEResultsUI0.0020.0010.002
getDataAssesmentText0.0020.0000.003
getDataForTables0.0010.0000.001
getDataPreparationText0.0020.0000.002
getDensityPlot0.0010.0000.001
getDensityPlotUI0.0000.0000.001
getDomains000
getDown0.0000.0000.001
getDownloadSection0.0130.0000.013
getEnrichDO000
getEnrichGO0.0000.0000.001
getEnrichKEGG0.0000.0000.001
getEntrezIds000
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0190.0000.019
getGOPlots0.0010.0000.001
getGSEA0.0010.0000.001
getGeneList0.8210.0890.914
getGeneSetData0.0000.0010.001
getGoPanel0.0310.0020.033
getGroupSelector0.0000.0000.001
getHeatmapUI0.0000.0000.001
getHelpButton000
getHideLegendOnOff0.0030.0000.004
getHistogramUI0.0010.0000.000
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0020.0000.002
getJSLine0.0030.0010.004
getKEGGModal0.0050.0000.006
getLeftMenu0.0010.0010.001
getLegendColors0.0020.0000.002
getLegendRadio0.0040.0000.004
getLegendSelect0.0030.0000.003
getLevelOrder0.0010.0000.000
getLoadingMsg0.0030.0010.003
getLogo0.0020.0010.002
getMainPanel0.0010.0000.002
getMainPlotUI000
getMainPlotsLeftMenu0.1310.0030.134
getMean000
getMergedComparison0.0000.0010.001
getMetaSelector0.0010.0000.000
getMethodDetails0.0010.0010.001
getMostVariedList0.0010.0000.000
getNormalizedMatrix0.0250.0020.027
getOrganism0.0000.0000.001
getOrganismBox0.0040.0000.004
getOrganismPathway0.0000.0000.001
getPCAPlotUI000
getPCAcontolUpdatesJS0.0010.0000.000
getPCAexplained4.1160.1374.327
getPCselection0.0010.0000.001
getPlotArea000
getProgramTitle0.0000.0000.001
getQAText0.0030.0010.003
getQCLeftMenu000
getQCPanel0.0050.0010.006
getSampleDetails0.0000.0000.001
getSampleNames0.0010.0000.001
getSamples0.0010.0000.000
getSearchData0.0000.0000.001
getSelHeat0.0000.0000.001
getSelectInputBox000
getSelectedCols0.0000.0000.001
getSelectedDatasetInput000
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0030.0000.004
getStartupMsg0.0030.0000.003
getTabUpdateJS0.0000.0000.001
getTableDetails0.0010.0010.001
getTableModal0.0110.0010.013
getTableStyle000
getUp0.0000.0000.001
getUpDown0.0000.0010.000
getVariationData0.0000.0000.001
get_conditions_given_selection0.0000.0010.000
heatmapControlsUI0.0680.0020.071
heatmapJScode000
heatmapServer0.0010.0000.001
heatmapUI0.1290.0050.135
hideObj0.0010.0000.000
histogramControlsUI0.0010.0000.000
installpack000
kmeansControlsUI0.0090.0010.010
lcfMetRadio0.0040.0000.004
loadpack0.0180.0330.053
mainPlotControlsUI0.0110.0010.011
mainScatterNew0.0010.0000.001
niceKmeans0.0000.0000.001
normalizationMethods0.0040.0000.004
palUI0.0040.0000.004
panel.cor0.0010.0000.001
panel.hist0.0020.0000.002
pcaPlotControlsUI0.0080.0000.009
plotData0.0010.0000.001
plotMarginsUI0.010.000.01
plotSizeMarginsUI0.0160.0000.017
plotSizeUI0.0050.0010.005
plotTypeUI0.0000.0000.001
plot_pca1.6050.0481.655
prepDEOutput000
prepDataContainer0.0010.0010.001
prepGroup0.0010.0000.001
prepHeatData0.0010.0000.001
prepPCADat000
push000
removeCols0.0000.0000.001
removeExtraCols0.0020.0000.003
round_vals000
runDE0.0000.0000.001
runDESeq2000
runEdgeR0.0010.0010.002
runHeatmap0.0010.0000.001
runHeatmap20.0010.0000.001
runLimma0.0010.0000.001
run_pca1.4050.0341.441
selectConditions0.0010.0000.001
selectGroupInfo0.0000.0010.001
selectedInput000
sepRadio0.0040.0000.004
setBatch0.0000.0000.001
showObj0.0000.0000.001
startDEBrowser000
startHeatmap0.0010.0000.001
textareaInput0.0010.0000.001
togglePanels0.0000.0000.001