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This page was generated on 2024-04-17 11:37:39 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 510/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.30.2  (landing page)
Alper Kucukural
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_18
git_last_commit: edf9f4c
git_last_commit_date: 2024-02-05 11:10:13 -0400 (Mon, 05 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for debrowser on merida1


To the developers/maintainers of the debrowser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/debrowser.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: debrowser
Version: 1.30.2
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_1.30.2.tar.gz
StartedAt: 2024-04-16 01:39:39 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 01:53:01 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 802.0 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_1.30.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/debrowser.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.30.2’
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkCountData : <anonymous>: no visible binding for global variable
  ‘err’
debrowserdataload: no visible binding for global variable ‘demodata’
debrowserhistogram: no visible global function definition for ‘config’
generateTestData: no visible binding for global variable ‘metadata’
getBarMainPlot: no visible global function definition for ‘config’
getBoxMainPlot: no visible global function definition for ‘config’
getDensityPlot: no visible binding for global variable ‘samples’
getDensityPlot: no visible global function definition for ‘config’
getGOPlots: no visible global function definition for ‘facet_grid’
getGSEA: no visible global function definition for ‘is’
getIQRPlot: no visible global function definition for ‘config’
mainScatterNew: no visible global function definition for ‘config’
plot_pca: no visible binding for global variable ‘x’
plot_pca: no visible binding for global variable ‘y’
plot_pca: no visible binding for global variable ‘textName’
plot_pca: no visible global function definition for ‘config’
runHeatmap: no visible global function definition for ‘config’
Undefined global functions or variables:
  config demodata err facet_grid is metadata samples textName x y
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-demo.R’
  Running ‘test-deseq.R’
  Running ‘test-null.R’
  Running ‘test-ui.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes 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-3.18-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/4.3-x86_64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 v1.30.2  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 
 27.918   1.765  31.548

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 v1.30.2  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 
 67.465   2.123  75.347

debrowser.Rcheck/tests/test-null.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 v1.30.2  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 
 27.319   1.772  32.481

debrowser.Rcheck/tests/test-ui.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 v1.30.2  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 
 27.511   1.834  32.212

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0320.0060.044
IQRPlotControlsUI0.0020.0000.003
actionButtonDE0.0070.0010.007
addDataCols0.0000.0000.001
addID0.0010.0000.000
all2all0.2790.0120.321
all2allControlsUI0.0580.0090.075
applyFilters0.0000.0000.001
applyFiltersNew0.0010.0000.001
applyFiltersToMergedComparison0.0000.0000.001
barMainPlotControlsUI0.0030.0010.004
batchEffectUI0.0810.0100.097
batchMethod0.0030.0000.004
changeClusterOrder0.0010.0000.001
checkCountData0.0000.0000.001
checkMetaData0.0010.0010.001
clustFunParamsUI0.0000.0010.001
clusterData0.0000.0010.003
compareClust0.0010.0010.001
condSelectUI0.0090.0010.010
correctCombat0.0010.0000.001
correctHarman000
customColorsUI0.0090.0010.013
cutOffSelectionUI0.0080.0010.008
dataLCFUI0.0220.0020.025
dataLoadUI0.0230.0020.026
deServer0.0150.0070.022
deUI0.2000.0100.226
debrowserIQRplot0.0000.0010.001
debrowserall2all0.0010.0010.001
debrowserbarmainplot000
debrowserbatcheffect0.0010.0000.002
debrowserboxmainplot000
debrowsercondselect0.0010.0010.001
debrowserdataload0.0010.0010.002
debrowserdeanalysis0.0010.0010.001
debrowserdensityplot0.0000.0010.003
debrowserheatmap0.0010.0010.001
debrowserhistogram0.0000.0010.001
debrowserlowcountfilter0.0010.0000.002
debrowsermainplot0.0010.0000.002
debrowserpcaplot0.0010.0000.001
dendControlsUI0.0120.0010.015
densityPlotControlsUI0.0030.0010.003
distFunParamsUI0.0000.0010.000
drawKEGG0.0000.0000.001
drawPCAExplained0.0000.0000.001
fileTypes000
fileUploadBox0.0060.0010.008
generateTestData0.0000.0000.002
getAfterLoadMsg0.0010.0000.002
getAll2AllPlotUI0.0010.0010.001
getBSTableUI0.0000.0010.001
getBarMainPlot0.0010.0000.001
getBarMainPlotUI0.0000.0000.001
getBoxMainPlot0.0010.0000.001
getBoxMainPlotUI0.0010.0010.001
getColorShapeSelection0.0000.0010.001
getColors0.0000.0010.001
getCompSelection0.0040.0000.004
getCondMsg0.0000.0000.001
getConditionSelector0.0010.0000.001
getConditionSelectorFromMeta0.0000.0010.001
getCovariateDetails0.0000.0010.001
getCutOffSelection0.0040.0010.004
getDEAnalysisText0.0040.0000.005
getDEResultsUI0.0030.0000.003
getDataAssesmentText0.0030.0000.003
getDataForTables0.0010.0010.001
getDataPreparationText0.0020.0000.003
getDensityPlot0.0010.0000.001
getDensityPlotUI000
getDomains000
getDown000
getDownloadSection0.0150.0010.017
getEnrichDO0.0000.0010.001
getEnrichGO0.0000.0000.001
getEnrichKEGG0.0010.0000.001
getEntrezIds0.0000.0000.001
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0200.0010.023
getGOPlots0.0010.0000.001
getGSEA0.0000.0000.001
getGeneList1.4020.2111.872
getGeneSetData0.0010.0000.001
getGoPanel0.0230.0010.030
getGroupSelector0.0010.0010.001
getHeatmapUI0.0010.0000.002
getHelpButton0.0000.0000.001
getHideLegendOnOff0.0030.0000.006
getHistogramUI0.0010.0000.001
getIQRPlot0.0010.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0030.0010.004
getJSLine0.0040.0010.006
getKEGGModal0.0060.0000.007
getLeftMenu0.0000.0010.005
getLegendColors0.0010.0010.001
getLegendRadio0.0060.0010.007
getLegendSelect0.0030.0010.012
getLevelOrder0.0010.0000.000
getLoadingMsg0.0030.0010.005
getLogo0.0020.0010.005
getMainPanel0.0030.0000.003
getMainPlotUI0.0000.0010.004
getMainPlotsLeftMenu0.1470.0030.178
getMean0.0010.0000.001
getMergedComparison0.0000.0010.001
getMetaSelector0.0010.0000.002
getMethodDetails0.0000.0010.001
getMostVariedList0.0010.0000.002
getNormalizedMatrix0.0250.0030.030
getOrganism0.0000.0000.001
getOrganismBox0.0040.0010.007
getOrganismPathway0.0000.0010.001
getPCAPlotUI0.0010.0010.001
getPCAcontolUpdatesJS0.0000.0010.001
getPCAexplained3.6050.1864.123
getPCselection0.0010.0000.002
getPlotArea0.0010.0010.001
getProgramTitle0.0000.0000.001
getQAText0.0030.0010.003
getQCLeftMenu0.0000.0000.001
getQCPanel0.0070.0010.008
getSampleDetails0.0000.0010.001
getSampleNames0.0010.0000.001
getSearchData0.0000.0010.001
getSelHeat0.0000.0010.001
getSelectInputBox0.0010.0000.001
getSelectedCols0.0000.0010.001
getSelectedDatasetInput0.0010.0000.001
getShapeColor0.0000.0000.001
getStartPlotsMsg0.0040.0010.005
getStartupMsg0.0040.0000.004
getTabUpdateJS0.0000.0010.001
getTableDetails0.0010.0010.001
getTableModal0.0060.0010.009
getTableStyle0.0000.0010.001
getUp0.0010.0000.001
getUpDown0.0000.0000.001
getVariationData0.0000.0010.001
get_conditions_given_selection0.0010.0000.001
heatmapControlsUI0.0720.0010.075
heatmapJScode0.0000.0010.000
heatmapServer0.0010.0020.003
heatmapUI0.1300.0030.148
hideObj0.0000.0000.001
histogramControlsUI0.0010.0000.001
installpack0.0010.0000.000
kmeansControlsUI0.0090.0000.010
lcfMetRadio0.0040.0010.004
loadpack0.0220.0540.083
mainPlotControlsUI0.0100.0000.013
mainScatterNew0.0010.0010.001
niceKmeans0.0000.0010.002
normalizationMethods0.0040.0000.006
palUI0.0050.0010.005
panel.cor0.0010.0010.003
panel.hist0.0020.0000.001
pcaPlotControlsUI0.0090.0010.012
plotData0.0000.0000.001
plotMarginsUI0.0100.0000.011
plotSizeMarginsUI0.0170.0010.019
plotSizeUI0.0050.0010.007
plotTypeUI0.0010.0000.001
plot_pca1.7860.0512.008
prepDataContainer0.0010.0000.002
prepGroup0.0000.0000.001
prepHeatData0.0010.0000.001
prepPCADat0.0000.0010.000
push0.0000.0010.000
removeCols0.0000.0010.001
removeExtraCols0.0030.0000.003
round_vals0.0010.0000.001
runDE0.0000.0000.001
runDESeq20.0010.0000.002
runEdgeR0.0010.0010.003
runHeatmap0.0010.0010.002
runHeatmap20.0010.0000.002
runLimma0.0010.0000.002
run_pca1.5370.0291.699
selectConditions0.0010.0000.002
selectGroupInfo0.0000.0010.001
selectedInput0.0000.0010.000
sepRadio0.0050.0010.005
setBatch000
showObj0.0000.0000.001
startDEBrowser0.0010.0000.001
startHeatmap0.0000.0010.001
textareaInput0.0010.0000.001
togglePanels0.0000.0000.001