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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 515/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.34.0  (landing page)
Alper Kucukural
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_20
git_last_commit: e323fef
git_last_commit_date: 2024-10-29 10:08:44 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped


CHECK results for debrowser on lconway

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: 1.34.0
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_1.34.0.tar.gz
StartedAt: 2024-11-19 21:14:32 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 21:23:55 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 562.7 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_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/debrowser.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.34.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 whether 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 ... 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-3.20-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/4.4-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.34.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("demo data can be loaded", {
+     load(system.file("extdata", "demo", "demodata.Rda",
+         package = "debrowser"))
+     expect_true(is.data.frame(demodata))
+     expect_equal(demodata[29311, 2], 2)
+     expect_equal(demodata[29311, 5], 7.1)
+     expect_equal(demodata[29311, 6], 6)
+     expect_null(demodata[1, 7])
+ })
Test passed 🎊
> 
> proc.time()
   user  system elapsed 
 13.186   0.997  14.284 

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.34.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> load(system.file("extdata", "demo", "demodata.Rda",
+     package = "debrowser"))
> metadata <- metadatatable 
> columns <- c("exper_rep1", "exper_rep2", "exper_rep3",
+     "control_rep1", "control_rep2", "control_rep3")
> conds <- factor( c("Control", "Control", "Control",
+     "Treat", "Treat", "Treat") )
> data <- data.frame(demodata[, columns])
> 
> #Run DESeq2 with the following parameters
> params <- c("DESeq2", "NoCovariate", "parametric", F, "Wald", "None") 
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+     deseqrun <- runDE(data, metadata, columns, conds, params)
+     expect_true(exists("deseqrun"))
+ })
Test passed 🌈
> 
> ##################################################
> deseqrun <- runDE(data, metadata, columns, conds, params)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> 
> de_res <- data.frame(deseqrun)
> norm_data <- getNormalizedMatrix(data[, columns])
> rdata <- cbind(rownames(de_res), norm_data[rownames(de_res), columns],
+                 log10(rowMeans(norm_data[rownames(de_res),
+                 paste(c("exper_rep1", "exper_rep2", "exper_rep3"))])
+                 + 0.1), log10( rowMeans( norm_data[ rownames( de_res ),
+                 paste(c("control_rep1", "control_rep2", "control_rep3"))])
+                 + 0.1), de_res[rownames(de_res),
+                 c("padj", "log2FoldChange")], 2 ^ de_res[rownames(de_res),
+                 "log2FoldChange"], -1 *
+                 log10(de_res[rownames(de_res), "padj"]))
> colnames(rdata) <- c("ID", columns, "Cond1", "Cond2", "padj",
+                 "log2FoldChange", "foldChange", "log10padj")
> rdata <- as.data.frame(rdata)
> rdata$padj[is.na(rdata$padj)] <- 1
> 
> padj_cutoff <- 0.01
> foldChange_cutoff <- 2
> 
> rdata$Legend <- character(nrow(rdata))
> rdata$Legend[rdata$log2FoldChange > log2(foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Up"
> rdata$Legend[rdata$log2FoldChange < log2(1 / foldChange_cutoff) &
+         rdata$padj < padj_cutoff] <- "Down"
> rdata$Legend[abs(rdata$log2FoldChange) <= 
+         log2(foldChange_cutoff)] <- "NS"
> rdata$Legend[is.null(rdata$log10padj)] <- "NA"
> rdata$Size <- character(nrow(rdata))
> rdata[, "Size"] <- "40"
> 
> dat <- rdata
> dat$M <- rdata$Cond1 - rdata$Cond2
> dat$A <- (rdata$Cond1 + rdata$Cond2) / 2
> 
> updown <- rdata[rdata$Legend=="Up" | rdata$Legend=="Down",columns]
> ##################################################
> 
> 
> 
> proc.time()
   user  system elapsed 
 31.676   1.420  33.274 

debrowser.Rcheck/tests/test-null.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.34.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("passing no data returns NULL", {
+     expect_null(compareClust() )
+     expect_null(getGOPlots(NULL, NULL))
+     null_deseq <- runDE(NULL)
+     expect_null(null_deseq)
+     expect_null(plot_pca(NULL))
+ })
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
 14.292   1.124  15.538 

debrowser.Rcheck/tests/test-ui.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 v1.34.0  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, Manuel Garber
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
BMC Genomics 2019 20:6

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("able to create panel UI", {
+     expect_silent( QCPanel <- getQCPanel() )
+     expect_true(exists("QCPanel"))
+     expect_equal(QCPanel[[1]][[1]], "div")
+ 
+     expect_silent( downloads <- getDownloadSection() )
+     expect_true(exists("downloads"))
+     expect_equal(downloads[[1]][[1]], "div")
+ 
+     expect_silent( getMain <- getMainPanel() )
+     expect_true(exists("getMain"))
+     expect_equal(getMain[[1]][[1]], "div")
+ 
+     expect_silent( getStart <- getStartupMsg() )
+     expect_true(exists("getStart"))
+     expect_equal(getStart[[1]][[1]], "div")
+ 
+     expect_silent( getAfter <- getAfterLoadMsg() )
+     expect_true(exists("getAfter"))
+     expect_equal(getAfter[[1]][[1]], "div")
+ 
+     expect_silent(getGO <- getGoPanel() )
+     expect_true(exists("getGO"))
+     expect_equal(getGO[[1]][[1]], "div")
+ })
Test passed 😀
> 
> proc.time()
   user  system elapsed 
 14.483   1.085  15.650 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0210.0040.025
IQRPlotControlsUI0.0010.0000.001
actionButtonDE0.0040.0010.004
addDataCols0.0000.0000.001
addID0.0010.0000.000
all2all0.1140.0070.121
all2allControlsUI0.0310.0070.039
applyFilters0.0010.0000.001
applyFiltersNew000
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0010.002
batchEffectUI0.0390.0080.048
batchMethod0.0020.0010.002
changeClusterOrder0.0010.0000.000
checkCountData000
checkMetaData000
clustFunParamsUI0.0010.0010.000
clusterData0.0000.0000.001
compareClust0.0000.0010.001
condSelectUI0.0040.0000.004
correctCombat0.0010.0000.000
correctHarman0.0010.0000.001
customColorsUI0.0040.0000.005
cutOffSelectionUI0.0040.0000.004
dataLCFUI0.0100.0010.011
dataLoadUI0.0090.0010.009
deServer0.0060.0020.008
deUI0.0890.0140.103
debrowserIQRplot000
debrowserall2all0.0010.0000.000
debrowserbarmainplot000
debrowserbatcheffect0.0000.0010.001
debrowserboxmainplot0.0000.0000.001
debrowsercondselect0.0000.0000.001
debrowserdataload0.0010.0000.001
debrowserdeanalysis0.0000.0010.000
debrowserdensityplot000
debrowserheatmap0.0000.0000.001
debrowserhistogram0.0010.0000.001
debrowserlowcountfilter000
debrowsermainplot0.0000.0000.001
debrowserpcaplot0.0000.0000.001
dendControlsUI0.0070.0010.007
densityPlotControlsUI0.0010.0000.001
distFunParamsUI000
drawKEGG000
drawPCAExplained000
fileTypes000
fileUploadBox0.0020.0010.003
generateTestData0.0010.0000.000
getAfterLoadMsg0.0010.0000.001
getAll2AllPlotUI0.0000.0000.001
getBSTableUI000
getBarMainPlot000
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI000
getColorShapeSelection0.0000.0010.001
getColors0.0010.0000.000
getCompSelection0.0020.0010.002
getCondMsg0.0000.0010.001
getConditionSelector000
getConditionSelectorFromMeta0.0010.0010.000
getCovariateDetails0.0000.0000.001
getCutOffSelection0.0010.0010.002
getDEAnalysisText0.0020.0010.002
getDEResultsUI0.0020.0000.001
getDataAssesmentText0.0010.0000.001
getDataForTables0.0010.0000.000
getDataPreparationText0.0010.0000.001
getDensityPlot0.0010.0010.001
getDensityPlotUI0.0000.0000.001
getDomains000
getDown0.0010.0000.000
getDownloadSection0.0090.0010.009
getEnrichDO0.0000.0000.001
getEnrichGO000
getEnrichKEGG0.0000.0000.001
getEntrezIds0.0000.0010.001
getEntrezTable0.0010.0000.000
getGOLeftMenu0.0110.0010.012
getGOPlots0.0010.0000.001
getGSEA0.0000.0010.000
getGeneList0.7780.1340.934
getGeneSetData0.0010.0000.000
getGoPanel0.0110.0010.012
getGroupSelector000
getHeatmapUI0.0000.0000.001
getHelpButton000
getHideLegendOnOff0.0020.0000.001
getHistogramUI0.0010.0000.000
getIQRPlot0.0000.0000.001
getIQRPlotUI0.0000.0000.001
getIntroText0.0020.0000.001
getJSLine0.0020.0010.002
getKEGGModal0.0020.0000.002
getLeftMenu0.0000.0010.001
getLegendColors0.0000.0000.001
getLegendRadio0.0020.0010.002
getLegendSelect0.0020.0000.002
getLevelOrder0.0000.0010.000
getLoadingMsg0.0010.0010.002
getLogo0.0010.0010.002
getMainPanel0.0010.0000.001
getMainPlotUI000
getMainPlotsLeftMenu0.0600.0020.061
getMean0.0000.0010.001
getMergedComparison0.0000.0000.001
getMetaSelector0.0010.0000.001
getMethodDetails000
getMostVariedList000
getNormalizedMatrix0.0130.0010.014
getOrganism0.0000.0000.001
getOrganismBox0.0020.0000.002
getOrganismPathway000
getPCAPlotUI0.0010.0000.000
getPCAcontolUpdatesJS000
getPCAexplained1.7320.0941.833
getPCselection0.0000.0010.001
getPlotArea0.0000.0000.001
getProgramTitle0.0010.0000.000
getQAText0.0010.0000.002
getQCLeftMenu0.0010.0010.000
getQCPanel0.0040.0010.005
getSampleDetails0.0010.0000.000
getSampleNames0.0000.0010.001
getSearchData0.0000.0000.001
getSelHeat0.0000.0010.000
getSelectInputBox0.0000.0000.001
getSelectedCols000
getSelectedDatasetInput0.0000.0000.001
getShapeColor0.0010.0000.000
getStartPlotsMsg0.0020.0010.003
getStartupMsg0.0030.0010.003
getTabUpdateJS0.0000.0000.001
getTableDetails0.0000.0000.001
getTableModal0.0030.0000.004
getTableStyle0.0000.0000.001
getUp000
getUpDown0.0000.0010.001
getVariationData0.0010.0000.000
get_conditions_given_selection0.0000.0000.001
heatmapControlsUI0.0340.0040.038
heatmapJScode000
heatmapServer0.0010.0010.002
heatmapUI0.0570.0090.066
hideObj0.0010.0000.000
histogramControlsUI0.0000.0000.001
installpack0.0000.0000.001
kmeansControlsUI0.0050.0000.006
lcfMetRadio0.0030.0000.003
loadpack0.0120.0250.037
mainPlotControlsUI0.0050.0010.005
mainScatterNew0.0010.0000.001
niceKmeans0.0010.0000.001
normalizationMethods0.0010.0010.002
palUI0.0020.0010.002
panel.cor0.0010.0010.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0040.0010.006
plotData0.0000.0010.001
plotMarginsUI0.0040.0010.005
plotSizeMarginsUI0.0070.0020.008
plotSizeUI0.0020.0010.003
plotTypeUI000
plot_pca0.6990.0400.758
prepDataContainer0.0010.0000.001
prepGroup0.0000.0010.000
prepHeatData000
prepPCADat000
push000
removeCols0.0000.0010.000
removeExtraCols0.0010.0000.001
round_vals0.0010.0000.000
runDE0.0000.0000.001
runDESeq20.0010.0000.001
runEdgeR0.0010.0000.000
runHeatmap0.0000.0010.000
runHeatmap2000
runLimma0.0010.0000.001
run_pca0.5560.0260.585
selectConditions0.0000.0000.002
selectGroupInfo0.0000.0010.001
selectedInput000
sepRadio0.0020.0010.002
setBatch000
showObj000
startDEBrowser0.0010.0000.000
startHeatmap0.0000.0000.001
textareaInput0.0000.0010.000
togglePanels0.0000.0000.001