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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 504/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.28.3  (landing page)
Alper Kucukural
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: RELEASE_3_17
git_last_commit: f25c541
git_last_commit_date: 2023-07-16 18:03:41 -0400 (Sun, 16 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for debrowser on kjohnson2


To the developers/maintainers of the debrowser package:
- 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: 1.28.3
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_1.28.3.tar.gz
StartedAt: 2023-10-17 14:12:06 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 14:22:19 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 613.1 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_1.28.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/debrowser.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.28.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘debrowser’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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-3.17-bioc-mac-arm64/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-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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 v1.28.3  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

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

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("demo data can be loaded", {
+     load(system.file("extdata", "demo", "demodata.Rda",
+         package = "debrowser"))
+     expect_true(is.data.frame(demodata))
+     expect_equal(demodata[29311, 2], 2)
+     expect_equal(demodata[29311, 5], 7.1)
+     expect_equal(demodata[29311, 6], 6)
+     expect_null(demodata[1, 7])
+ })
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
 15.101   0.899  24.509

debrowser.Rcheck/tests/test-deseq.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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 v1.28.3  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

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

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> load(system.file("extdata", "demo", "demodata.Rda",
+     package = "debrowser"))
> 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 
 36.205   1.221  56.249

debrowser.Rcheck/tests/test-null.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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 v1.28.3  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

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

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("passing no data returns NULL", {
+     expect_null(compareClust() )
+     expect_null(getGOPlots(NULL, NULL))
+     null_deseq <- runDE(NULL)
+     expect_null(null_deseq)
+     expect_null(plot_pca(NULL))
+ })
Test passed 🥇
> 
> proc.time()
   user  system elapsed 
 15.167   0.937  23.853

debrowser.Rcheck/tests/test-ui.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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 v1.28.3  For help: https://debrowser.readthedocs.org/

If you use DEBrowser in published research, please cite:

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

doi:0.1186/s12864-018-5362-x

> library(testthat)
> 
> test_that("able to create panel UI", {
+     expect_silent( QCPanel <- getQCPanel() )
+     expect_true(exists("QCPanel"))
+     expect_equal(QCPanel[[1]][[1]], "div")
+ 
+     expect_silent( downloads <- getDownloadSection() )
+     expect_true(exists("downloads"))
+     expect_equal(downloads[[1]][[1]], "div")
+ 
+     expect_silent( getMain <- getMainPanel() )
+     expect_true(exists("getMain"))
+     expect_equal(getMain[[1]][[1]], "div")
+ 
+     expect_silent( getStart <- getStartupMsg() )
+     expect_true(exists("getStart"))
+     expect_equal(getStart[[1]][[1]], "div")
+ 
+     expect_silent( getAfter <- getAfterLoadMsg() )
+     expect_true(exists("getAfter"))
+     expect_equal(getAfter[[1]][[1]], "div")
+ 
+     expect_silent(getGO <- getGoPanel() )
+     expect_true(exists("getGO"))
+     expect_equal(getGO[[1]][[1]], "div")
+ })
Test passed 😀
> 
> proc.time()
   user  system elapsed 
 15.209   0.968  24.829

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0250.0040.041
IQRPlotControlsUI0.0010.0000.002
actionButtonDE0.0040.0010.008
addDataCols000
addID000
all2all0.8440.0151.309
all2allControlsUI0.0290.0060.049
applyFilters0.0000.0010.001
applyFiltersNew0.0000.0010.000
applyFiltersToMergedComparison0.0000.0000.001
barMainPlotControlsUI0.0020.0000.002
batchEffectUI0.0450.0070.073
batchMethod0.0020.0000.002
changeClusterOrder0.0000.0000.001
checkCountData0.0010.0000.000
checkMetaData0.0000.0010.001
clustFunParamsUI000
clusterData000
compareClust0.0010.0000.001
condSelectUI0.0050.0000.006
correctCombat0.0010.0000.000
correctHarman0.0000.0010.001
customColorsUI0.0060.0020.012
cutOffSelectionUI0.0040.0000.007
dataLCFUI0.0110.0010.018
dataLoadUI0.0100.0010.016
deServer0.0090.0020.016
deUI0.0990.0070.162
debrowserIQRplot0.0000.0010.001
debrowserall2all000
debrowserbarmainplot000
debrowserbatcheffect0.0000.0000.001
debrowserboxmainplot0.0000.0010.000
debrowsercondselect0.0000.0000.001
debrowserdataload0.0010.0000.002
debrowserdeanalysis0.0000.0010.001
debrowserdensityplot0.0000.0000.001
debrowserheatmap0.0010.0000.001
debrowserhistogram0.0010.0010.001
debrowserlowcountfilter0.0010.0000.001
debrowsermainplot0.0000.0000.001
debrowserpcaplot0.0000.0000.001
dendControlsUI0.0070.0010.012
densityPlotControlsUI0.0010.0010.005
distFunParamsUI000
drawKEGG0.0010.0000.001
drawPCAExplained0.0010.0010.001
fileTypes0.0000.0000.002
fileUploadBox0.0030.0000.004
generateTestData0.0000.0000.001
getAfterLoadMsg0.0000.0010.000
getAll2AllPlotUI0.0010.0000.003
getBSTableUI000
getBarMainPlot0.0010.0000.001
getBarMainPlotUI0.0010.0010.001
getBoxMainPlot0.0010.0000.001
getBoxMainPlotUI0.0010.0000.001
getColorShapeSelection0.0010.0000.000
getColors0.0010.0000.003
getCompSelection0.0020.0000.002
getCondMsg0.0000.0000.001
getConditionSelector0.0000.0000.001
getConditionSelectorFromMeta0.0010.0010.003
getCovariateDetails0.0010.0000.000
getCutOffSelection0.0020.0000.005
getDEAnalysisText0.0020.0000.004
getDEResultsUI0.0010.0010.001
getDataAssesmentText0.0020.0000.002
getDataForTables0.0000.0000.001
getDataPreparationText0.0010.0010.002
getDensityPlot000
getDensityPlotUI0.0000.0000.001
getDomains000
getDown0.0010.0000.001
getDownloadSection0.0080.0000.014
getEnrichDO0.0000.0000.002
getEnrichGO000
getEnrichKEGG0.0010.0010.001
getEntrezIds0.0010.0000.000
getEntrezTable0.0000.0000.001
getGOLeftMenu0.0130.0010.022
getGOPlots0.0010.0000.001
getGSEA0.0010.0010.003
getGeneList0.6270.1101.117
getGeneSetData0.0010.0000.001
getGoPanel0.0110.0020.018
getGroupSelector0.0000.0000.001
getHeatmapUI0.0000.0000.001
getHelpButton0.0010.0000.004
getHideLegendOnOff0.0030.0000.003
getHistogramUI0.0010.0010.000
getIQRPlot0.0000.0000.001
getIQRPlotUI000
getIntroText0.0010.0000.001
getJSLine0.0030.0000.006
getKEGGModal0.0030.0000.004
getLeftMenu0.0010.0000.001
getLegendColors0.0010.0010.004
getLegendRadio0.0020.0010.005
getLegendSelect0.0020.0000.006
getLevelOrder000
getLoadingMsg0.0010.0010.004
getLogo0.0020.0000.005
getMainPanel0.0010.0000.002
getMainPlotUI0.0000.0000.001
getMainPlotsLeftMenu0.0860.0100.147
getMean000
getMergedComparison0.0010.0010.004
getMetaSelector0.0000.0000.001
getMethodDetails0.0000.0010.002
getMostVariedList0.0000.0000.001
getNormalizedMatrix0.0150.0020.029
getOrganism0.0010.0000.000
getOrganismBox0.0020.0000.004
getOrganismPathway0.0000.0000.001
getPCAPlotUI0.0000.0010.004
getPCAcontolUpdatesJS0.0000.0000.001
getPCAexplained1.9510.0723.072
getPCselection0.0010.0000.001
getPlotArea000
getProgramTitle0.0010.0000.001
getQAText0.0020.0000.004
getQCLeftMenu0.0010.0000.001
getQCPanel0.0030.0000.004
getSampleDetails0.0010.0000.000
getSampleNames0.0000.0000.001
getSearchData0.0010.0000.000
getSelHeat000
getSelectInputBox0.0000.0010.000
getSelectedCols0.0010.0000.001
getSelectedDatasetInput0.0000.0000.001
getShapeColor0.0000.0000.002
getStartPlotsMsg0.0020.0000.002
getStartupMsg0.0020.0000.002
getTabUpdateJS0.0000.0000.001
getTableDetails0.0000.0010.000
getTableModal0.0030.0000.006
getTableStyle0.0010.0000.001
getUp000
getUpDown0.0000.0010.000
getVariationData0.0000.0010.000
get_conditions_given_selection000
heatmapControlsUI0.0410.0010.065
heatmapJScode000
heatmapServer0.0010.0010.005
heatmapUI0.0680.0050.106
hideObj000
histogramControlsUI0.0000.0000.004
installpack0.0000.0010.000
kmeansControlsUI0.0050.0000.008
lcfMetRadio0.0020.0000.002
loadpack0.0150.0290.062
mainPlotControlsUI0.0060.0010.007
mainScatterNew0.0010.0010.001
niceKmeans0.0010.0000.001
normalizationMethods0.0020.0000.002
palUI0.0020.0010.002
panel.cor0.0010.0000.000
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0050.0010.008
plotData0.0010.0000.001
plotMarginsUI0.0050.0000.006
plotSizeMarginsUI0.0090.0000.012
plotSizeUI0.0030.0000.004
plotTypeUI0.0010.0000.001
plot_pca0.9520.0231.477
prepDataContainer0.0010.0000.001
prepGroup0.0010.0000.001
prepHeatData0.0010.0010.000
prepPCADat000
push0.0000.0000.001
removeCols0.0010.0000.000
removeExtraCols0.0020.0000.004
round_vals0.0010.0000.000
runDE000
runDESeq20.0000.0000.001
runEdgeR0.0010.0000.005
runHeatmap0.0010.0000.001
runHeatmap20.0010.0000.001
runLimma0.0010.0000.001
run_pca0.7830.0151.219
selectConditions0.0010.0000.001
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