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This page was generated on 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 509/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.33.0  (landing page)
Alper Kucukural
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/debrowser
git_branch: devel
git_last_commit: ec057cc
git_last_commit_date: 2024-04-30 10:49:26 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for debrowser on nebbiolo2

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: 1.33.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings debrowser_1.33.0.tar.gz
StartedAt: 2024-07-23 22:42:42 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 22:49:57 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 434.8 seconds
RetCode: 0
Status:   OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:debrowser.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings debrowser_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/debrowser.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.33.0’
* 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 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/debrowser.Rcheck/00check.log’
for details.


Installation output

debrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL debrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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-pc-linux-gnu

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 v1.33.0  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 
 14.345   0.790  15.124 

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-pc-linux-gnu

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 v1.33.0  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 
 32.767   0.955  33.712 

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-pc-linux-gnu

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 v1.33.0  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 
 13.962   0.834  14.785 

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-pc-linux-gnu

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 v1.33.0  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 
 13.995   0.865  14.848 

Example timings

debrowser.Rcheck/debrowser-Ex.timings

nameusersystemelapsed
BoxMainPlotControlsUI0.0200.0040.023
IQRPlotControlsUI0.0010.0010.002
actionButtonDE0.0040.0000.004
addDataCols000
addID0.0010.0000.000
all2all0.1280.0030.132
all2allControlsUI0.0290.0010.030
applyFilters000
applyFiltersNew000
applyFiltersToMergedComparison000
barMainPlotControlsUI0.0010.0000.001
batchEffectUI0.0350.0040.040
batchMethod0.0000.0010.002
changeClusterOrder0.0000.0010.000
checkCountData000
checkMetaData0.0000.0000.001
clustFunParamsUI0.0000.0010.000
clusterData000
compareClust0.0000.0000.001
condSelectUI0.0050.0000.004
correctCombat000
correctHarman000
customColorsUI0.0050.0000.004
cutOffSelectionUI0.0040.0000.003
dataLCFUI0.010.000.01
dataLoadUI0.010.000.01
deServer0.0060.0000.006
deUI0.0890.0070.096
debrowserIQRplot0.0010.0000.000
debrowserall2all000
debrowserbarmainplot0.0000.0000.001
debrowserbatcheffect0.0010.0000.000
debrowserboxmainplot000
debrowsercondselect000
debrowserdataload0.0010.0000.001
debrowserdeanalysis0.0000.0000.001
debrowserdensityplot000
debrowserheatmap000
debrowserhistogram000
debrowserlowcountfilter0.0000.0000.001
debrowsermainplot0.0010.0000.001
debrowserpcaplot0.0010.0000.001
dendControlsUI0.0070.0000.007
densityPlotControlsUI0.0020.0000.002
distFunParamsUI0.0000.0000.001
drawKEGG000
drawPCAExplained000
fileTypes000
fileUploadBox0.0030.0000.002
generateTestData0.0010.0000.000
getAfterLoadMsg000
getAll2AllPlotUI000
getBSTableUI0.0000.0000.001
getBarMainPlot0.0010.0000.000
getBarMainPlotUI000
getBoxMainPlot000
getBoxMainPlotUI0.0010.0000.001
getColorShapeSelection000
getColors000
getCompSelection0.0020.0000.002
getCondMsg0.0000.0000.001
getConditionSelector0.0010.0000.000
getConditionSelectorFromMeta000
getCovariateDetails000
getCutOffSelection0.0020.0000.002
getDEAnalysisText0.0010.0000.002
getDEResultsUI0.0010.0000.002
getDataAssesmentText0.0020.0000.002
getDataForTables000
getDataPreparationText0.0010.0000.001
getDensityPlot0.0010.0000.000
getDensityPlotUI000
getDomains0.0000.0000.001
getDown000
getDownloadSection0.0070.0000.008
getEnrichDO000
getEnrichGO000
getEnrichKEGG0.0000.0000.001
getEntrezIds000
getEntrezTable000
getGOLeftMenu0.0080.0020.010
getGOPlots0.0000.0000.001
getGSEA0.0000.0000.001
getGeneList0.7050.0410.747
getGeneSetData000
getGoPanel0.0120.0000.012
getGroupSelector0.0010.0000.000
getHeatmapUI000
getHelpButton000
getHideLegendOnOff0.0020.0000.002
getHistogramUI000
getIQRPlot000
getIQRPlotUI0.0000.0000.001
getIntroText0.0010.0000.001
getJSLine0.0010.0000.002
getKEGGModal0.0020.0000.002
getLeftMenu000
getLegendColors0.0010.0000.001
getLegendRadio0.0020.0000.002
getLegendSelect0.0010.0000.002
getLevelOrder0.0000.0000.001
getLoadingMsg0.0020.0000.002
getLogo0.0010.0000.001
getMainPanel0.0010.0000.001
getMainPlotUI000
getMainPlotsLeftMenu0.0640.0000.064
getMean000
getMergedComparison0.0010.0000.001
getMetaSelector000
getMethodDetails000
getMostVariedList000
getNormalizedMatrix0.0110.0040.015
getOrganism0.0000.0000.001
getOrganismBox0.0000.0020.002
getOrganismPathway0.0000.0000.001
getPCAPlotUI000
getPCAcontolUpdatesJS000
getPCAexplained2.0950.1512.247
getPCselection0.0010.0000.001
getPlotArea000
getProgramTitle000
getQAText0.0010.0000.001
getQCLeftMenu000
getQCPanel0.0030.0000.003
getSampleDetails000
getSampleNames000
getSearchData0.0010.0000.001
getSelHeat000
getSelectInputBox0.0010.0000.000
getSelectedCols000
getSelectedDatasetInput000
getShapeColor000
getStartPlotsMsg0.0020.0000.002
getStartupMsg0.0020.0000.002
getTabUpdateJS000
getTableDetails0.0010.0000.001
getTableModal0.0000.0030.003
getTableStyle000
getUp000
getUpDown000
getVariationData0.0010.0000.001
get_conditions_given_selection000
heatmapControlsUI0.0250.0080.033
heatmapJScode000
heatmapServer0.0010.0000.001
heatmapUI0.0560.0030.060
hideObj0.0010.0000.001
histogramControlsUI000
installpack000
kmeansControlsUI0.0050.0000.005
lcfMetRadio0.0020.0000.002
loadpack0.0000.0010.002
mainPlotControlsUI0.0030.0010.005
mainScatterNew0.0010.0010.001
niceKmeans0.0010.0000.001
normalizationMethods0.0020.0000.002
palUI0.0020.0000.002
panel.cor0.0010.0000.001
panel.hist0.0010.0000.001
pcaPlotControlsUI0.0010.0040.005
plotData000
plotMarginsUI0.0040.0000.004
plotSizeMarginsUI0.0080.0000.008
plotSizeUI0.0020.0000.002
plotTypeUI000
plot_pca0.7890.0470.836
prepDataContainer0.0010.0000.001
prepGroup0.0010.0010.001
prepHeatData000
prepPCADat0.0010.0000.001
push000
removeCols0.0000.0000.001
removeExtraCols0.0010.0000.001
round_vals000
runDE000
runDESeq2000
runEdgeR000
runHeatmap000
runHeatmap20.0010.0000.001
runLimma0.0010.0000.001
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