Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-19 11:05:57 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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? here 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 462/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.23.4  (landing page)
Alper Kucukural
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: master
git_last_commit: 0dcdc76
git_last_commit_date: 2021-12-15 18:12:31 -0500 (Wed, 15 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'annotate' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'DOSE' which is not available

Summary

Package: debrowser
Version: 1.23.4
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings debrowser_1.23.4.tar.gz
StartedAt: 2022-01-18 18:51:28 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 18:56:16 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 288.1 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings debrowser_1.23.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/debrowser.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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 ‘1.23.4’
* 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 ‘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 facet_grid 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/debrowser.Rcheck/00check.log’
for details.



Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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 v1.23.4  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 
 11.059   0.595  11.638 

debrowser.Rcheck/tests/test-deseq.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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 v1.23.4  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]
> ##################################################
> 
> test_that("Check the QC plots", {
+     expect_silent( all2all(data) )
+ })
Test passed 🎉
> 
> 
> proc.time()
   user  system elapsed 
 28.246   1.094  29.322 

debrowser.Rcheck/tests/test-null.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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 v1.23.4  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 
 11.201   0.530  11.718 

debrowser.Rcheck/tests/test-ui.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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 v1.23.4  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 
 11.499   0.589  12.071 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0220.0080.030
IQRPlotControlsUI0.0010.0000.002
actionButtonDE0.0030.0000.003
addDataCols000
addID0.0010.0000.000
all2all0.1100.0040.114
all2allControlsUI0.0270.0000.027
applyFilters0.0010.0000.001
applyFiltersNew0.0000.0000.001
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0000.001
batchEffectUI0.0350.0040.038
batchMethod0.0010.0000.002
changeClusterOrder0.0000.0000.001
checkCountData000
checkMetaData000
clustFunParamsUI0.0010.0000.000
clusterData0.0010.0000.000
compareClust0.0000.0000.001
condSelectUI0.0300.0000.031
correctCombat0.0000.0000.001
correctHarman0.0000.0000.001
customColorsUI0.0050.0000.006
cutOffSelectionUI0.0030.0000.003
dataLCFUI0.0150.0000.015
dataLoadUI0.0110.0000.012
deServer0.0040.0040.008
deUI0.0910.0040.095
debrowserIQRplot0.0000.0000.001
debrowserall2all0.0000.0000.001
debrowserbarmainplot000
debrowserbatcheffect0.0010.0000.001
debrowserboxmainplot0.0010.0000.000
debrowsercondselect0.0010.0000.000
debrowserdataload0.0010.0000.000
debrowserdeanalysis0.0010.0000.000
debrowserdensityplot000
debrowserheatmap000
debrowserhistogram000
debrowserlowcountfilter000
debrowsermainplot0.0010.0000.000
debrowserpcaplot0.0010.0000.000
dendControlsUI0.0050.0000.004
densityPlotControlsUI0.0010.0000.001
distFunParamsUI000
drawKEGG0.0010.0000.000
drawPCAExplained000
fileTypes000
fileUploadBox0.0000.0030.003
generateTestData0.0000.0010.001
getAfterLoadMsg0.0000.0010.001
getAll2AllPlotUI0.0000.0010.001
getBSTableUI0.0000.0000.001
getBarMainPlot000
getBarMainPlotUI000
getBoxMainPlot0.0010.0000.000
getBoxMainPlotUI000
getColorShapeSelection000
getColors0.0000.0000.001
getCompSelection0.0020.0000.002
getCondMsg0.0010.0000.001
getConditionSelector0.0010.0000.000
getConditionSelectorFromMeta0.0010.0000.000
getCovariateDetails000
getCutOffSelection0.0010.0000.001
getDEAnalysisText0.0010.0000.001
getDEResultsUI0.0010.0000.002
getDataAssesmentText0.0010.0000.002
getDataForTables0.0000.0000.001
getDataPreparationText0.0010.0000.001
getDensityPlot000
getDensityPlotUI000
getDomains0.0000.0000.001
getDown0.0010.0000.000
getDownloadSection0.0050.0000.005
getEnrichDO000
getEnrichGO000
getEnrichKEGG0.0000.0000.001
getEntrezIds0.0000.0010.001
getEntrezTable0.0000.0010.000
getGOLeftMenu0.0030.0030.007
getGOPlots000
getGSEA000
getGeneList0.3500.0440.393
getGeneSetData0.0010.0000.000
getGoPanel0.0160.0000.016
getGroupSelector0.0010.0000.000
getHeatmapUI0.0010.0000.000
getHelpButton000
getHideLegendOnOff0.0010.0000.002
getHistogramUI0.0000.0000.001
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0010.0000.000
getIntroText0.0010.0000.001
getJSLine0.0020.0000.001
getKEGGModal0.0030.0000.002
getLeftMenu0.0010.0000.000
getLegendColors0.0010.0000.001
getLegendRadio0.0010.0000.002
getLegendSelect0.0010.0000.001
getLevelOrder000
getLoadingMsg0.0000.0020.002
getLogo0.0000.0010.001
getMainPanel0.0000.0000.001
getMainPlotUI0.0000.0000.001
getMainPlotsLeftMenu0.0500.0000.051
getMean0.0000.0000.001
getMergedComparison0.0000.0000.001
getMetaSelector0.0000.0000.001
getMethodDetails0.0010.0000.001
getMostVariedList0.0000.0000.001
getNormalizedMatrix0.0120.0000.013
getOrganism000
getOrganismBox0.0020.0000.001
getOrganismPathway0.0010.0000.000
getPCAPlotUI000
getPCAcontolUpdatesJS000
getPCAexplained1.7780.0701.852
getPCselection0.0010.0000.001
getPlotArea000
getProgramTitle000
getQAText0.0010.0000.001
getQCLeftMenu0.0010.0000.000
getQCPanel0.0030.0000.002
getSampleDetails000
getSampleNames000
getSamples0.0010.0000.000
getSearchData0.0000.0000.001
getSelHeat0.0000.0000.001
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput000
getShapeColor0.0010.0000.000
getStartPlotsMsg0.0020.0000.002
getStartupMsg0.0010.0000.002
getTabUpdateJS0.0000.0000.001
getTableDetails0.0000.0000.001
getTableModal0.0060.0000.006
getTableStyle000
getTextOnOff0.0000.0010.001
getUp000
getUpDown0.0000.0000.001
getVariationData0.0000.0000.001
get_conditions_given_selection000
heatmapControlsUI0.0250.0000.025
heatmapJScode0.0010.0000.000
heatmapServer0.0010.0000.002
heatmapUI0.0520.0000.052
hideObj0.0010.0000.000
histogramControlsUI0.0000.0010.001
installpack0.0000.0010.000
kmeansControlsUI0.0020.0020.004
lcfMetRadio0.0010.0000.002
loadpack0.010.020.03
mainPlotControlsUI0.0050.0000.005
mainScatterNew0.0010.0000.001
niceKmeans0.0010.0000.000
normalizationMethods0.0020.0000.001
palUI0.0020.0000.001
panel.cor0.0010.0000.000
panel.hist0.0000.0000.001
pcaPlotControlsUI0.0020.0020.004
plotData000
plotMarginsUI0.0030.0000.003
plotSizeMarginsUI0.0060.0000.006
plotSizeUI0.0020.0000.002
plotTypeUI000
plot_pca0.7080.0160.725
prepDEOutput0.0000.0000.001
prepDataContainer0.0010.0000.001
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removeCols0.0010.0000.000
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round_vals0.0000.0000.001
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runDESeq2000
runEdgeR0.0000.0000.001
runHeatmap0.0010.0000.001
runHeatmap20.0000.0010.001
runLimma0.0000.0010.001
run_pca0.6230.0020.626
selectConditions0.0010.0000.001
selectGroupInfo000
selectedInput0.0010.0000.000
sepRadio0.0020.0000.002
setBatch000
showObj0.0010.0000.000
startDEBrowser0.0000.0000.001
startHeatmap000
textareaInput000
togglePanels000