Alper Kucukural
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/debrowser |
| Branch: RELEASE_3_11 |
| Last Commit: be42a8e |
| Last Changed Date: 2020-10-12 13:55:21 -0400 (Mon, 12 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:21 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE debrowser PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 431/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| debrowser 1.16.3 Alper Kucukural
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: debrowser |
| Version: 1.16.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings debrowser_1.16.3.tar.gz |
| StartedAt: 2020-10-17 00:18:51 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 00:27:50 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 538.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: debrowser.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:debrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings debrowser_1.16.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/debrowser.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘debrowser/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘debrowser’ version ‘1.16.3’ * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE checkCountData : <anonymous>: no visible binding for global variable ‘err’ debrowserdataload: no visible binding for global variable ‘demodata’ debrowserhistogram: no visible global function definition for ‘config’ getBarMainPlot: no visible global function definition for ‘config’ getBoxMainPlot: no visible global function definition for ‘config’ getDensityPlot: no visible binding for global variable ‘samples’ getDensityPlot: no visible global function definition for ‘config’ getIQRPlot: no visible global function definition for ‘config’ mainScatterNew: no visible global function definition for ‘config’ plot_pca: no visible binding for global variable ‘x’ plot_pca: no visible binding for global variable ‘y’ plot_pca: no visible binding for global variable ‘samples’ plot_pca: no visible global function definition for ‘config’ runHeatmap: no visible global function definition for ‘config’ Undefined global functions or variables: config demodata err samples x y * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-demo.R’ Running ‘test-deseq.R’ Running ‘test-null.R’ Running ‘test-ui.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.11-bioc/meat/debrowser.Rcheck/00check.log’ for details.
debrowser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL debrowser ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)
debrowser.Rcheck/tests/test-demo.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 v1.16.3 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])
+ })
>
> proc.time()
user system elapsed
20.121 1.366 21.482
debrowser.Rcheck/tests/test-deseq.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 v1.16.3 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"))
> 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])
> params <-
+ #Run DESeq2 with the following parameters
+ c("DESeq2", "parametric", F, "Wald")
> non_expressed_cutoff <- 10
> data <- subset(data, rowSums(data) > 10)
> test_that("Able to run DESeq2", {
+ deseqrun <- runDE(data, columns, conds, params)
+ expect_true(exists("deseqrun"))
+ })
>
> ##################################################
> deseqrun <- runDE(data, columns, conds, params)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
>
> de_res <- data.frame(deseqrun)
> norm_data <- getNormalizedMatrix(data[, columns])
> rdata <- cbind(rownames(de_res), norm_data[rownames(de_res), columns],
+ log10(rowMeans(norm_data[rownames(de_res),
+ paste(c("exper_rep1", "exper_rep2", "exper_rep3"))])
+ + 0.1), log10( rowMeans( norm_data[ rownames( de_res ),
+ paste(c("control_rep1", "control_rep2", "control_rep3"))])
+ + 0.1), de_res[rownames(de_res),
+ c("padj", "log2FoldChange")], 2 ^ de_res[rownames(de_res),
+ "log2FoldChange"], -1 *
+ log10(de_res[rownames(de_res), "padj"]))
> colnames(rdata) <- c("ID", columns, "Cond1", "Cond2", "padj",
+ "log2FoldChange", "foldChange", "log10padj")
> rdata <- as.data.frame(rdata)
> rdata$padj[is.na(rdata$padj)] <- 1
>
> padj_cutoff <- 0.01
> foldChange_cutoff <- 2
>
> rdata$Legend <- character(nrow(rdata))
> rdata$Legend[rdata$log2FoldChange > log2(foldChange_cutoff) &
+ rdata$padj < padj_cutoff] <- "Up"
> rdata$Legend[rdata$log2FoldChange < log2(1 / foldChange_cutoff) &
+ rdata$padj < padj_cutoff] <- "Down"
> rdata$Legend[abs(rdata$log2FoldChange) <=
+ log2(foldChange_cutoff)] <- "NS"
> rdata$Legend[is.null(rdata$log10padj)] <- "NA"
> rdata$Size <- character(nrow(rdata))
> rdata[, "Size"] <- "40"
>
> dat <- rdata
> dat$M <- rdata$Cond1 - rdata$Cond2
> dat$A <- (rdata$Cond1 + rdata$Cond2) / 2
>
> updown <- rdata[rdata$Legend=="Up" | rdata$Legend=="Down",columns]
> ##################################################
>
> test_that("Check the QC plots", {
+ expect_silent( all2all(data) )
+ })
>
>
> proc.time()
user system elapsed
51.652 1.941 53.608
debrowser.Rcheck/tests/test-null.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 v1.16.3 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))
+ })
>
> proc.time()
user system elapsed
20.187 1.440 21.622
debrowser.Rcheck/tests/test-ui.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 v1.16.3 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")
+ })
>
> proc.time()
user system elapsed
19.634 1.389 21.156
debrowser.Rcheck/debrowser-Ex.timings
| name | user | system | elapsed | |
| BoxMainPlotControlsUI | 0.004 | 0.001 | 0.005 | |
| IQRPlotControlsUI | 0.001 | 0.000 | 0.001 | |
| actionButtonDE | 0.006 | 0.000 | 0.006 | |
| addDataCols | 0.06 | 0.00 | 0.06 | |
| addID | 0 | 0 | 0 | |
| all2all | 0.240 | 0.006 | 0.245 | |
| all2allControlsUI | 0.003 | 0.000 | 0.003 | |
| applyFilters | 0.001 | 0.000 | 0.001 | |
| applyFiltersNew | 0.001 | 0.000 | 0.001 | |
| applyFiltersToMergedComparison | 0.000 | 0.001 | 0.001 | |
| barMainPlotControlsUI | 0.002 | 0.000 | 0.002 | |
| batchEffectUI | 0.069 | 0.005 | 0.074 | |
| batchMethod | 0.004 | 0.000 | 0.004 | |
| changeClusterOrder | 0.001 | 0.000 | 0.001 | |
| checkCountData | 0.000 | 0.001 | 0.001 | |
| checkMetaData | 0.000 | 0.000 | 0.001 | |
| clustFunParamsUI | 0.001 | 0.000 | 0.001 | |
| clusterData | 0.001 | 0.001 | 0.001 | |
| compareClust | 0 | 0 | 0 | |
| condSelectUI | 0.006 | 0.000 | 0.007 | |
| correctCombat | 0.001 | 0.001 | 0.001 | |
| correctHarman | 0.000 | 0.000 | 0.001 | |
| customColorsUI | 0.010 | 0.002 | 0.013 | |
| cutOffSelectionUI | 0.006 | 0.000 | 0.006 | |
| dataLCFUI | 0.028 | 0.003 | 0.032 | |
| dataLoadUI | 0.028 | 0.002 | 0.030 | |
| deServer | 0.019 | 0.005 | 0.024 | |
| deUI | 0.197 | 0.014 | 0.212 | |
| debrowserIQRplot | 0.001 | 0.000 | 0.000 | |
| debrowserall2all | 0.001 | 0.000 | 0.000 | |
| debrowserbarmainplot | 0.000 | 0.000 | 0.001 | |
| debrowserbatcheffect | 0.001 | 0.000 | 0.000 | |
| debrowserboxmainplot | 0.000 | 0.000 | 0.001 | |
| debrowsercondselect | 0 | 0 | 0 | |
| debrowserdataload | 0.001 | 0.000 | 0.001 | |
| debrowserdeanalysis | 0.000 | 0.000 | 0.001 | |
| debrowserdensityplot | 0.001 | 0.001 | 0.001 | |
| debrowserheatmap | 0.000 | 0.000 | 0.001 | |
| debrowserhistogram | 0.001 | 0.000 | 0.000 | |
| debrowserlowcountfilter | 0.001 | 0.001 | 0.001 | |
| debrowsermainplot | 0.000 | 0.000 | 0.001 | |
| debrowserpcaplot | 0.001 | 0.000 | 0.000 | |
| dendControlsUI | 0.011 | 0.000 | 0.011 | |
| densityPlotControlsUI | 0.001 | 0.001 | 0.002 | |
| distFunParamsUI | 0.001 | 0.000 | 0.001 | |
| drawKEGG | 0.001 | 0.000 | 0.001 | |
| drawPCAExplained | 0.000 | 0.000 | 0.001 | |
| fileTypes | 0.000 | 0.001 | 0.000 | |
| fileUploadBox | 0.003 | 0.000 | 0.003 | |
| generateTestData | 0.001 | 0.000 | 0.001 | |
| getAfterLoadMsg | 0.001 | 0.000 | 0.001 | |
| getAll2AllPlotUI | 0.001 | 0.000 | 0.000 | |
| getBSTableUI | 0.001 | 0.000 | 0.000 | |
| getBarMainPlot | 0.001 | 0.001 | 0.001 | |
| getBarMainPlotUI | 0 | 0 | 0 | |
| getBoxMainPlot | 0.000 | 0.001 | 0.000 | |
| getBoxMainPlotUI | 0 | 0 | 0 | |
| getColorShapeSelection | 0.000 | 0.001 | 0.000 | |
| getColors | 0.000 | 0.000 | 0.001 | |
| getCompSelection | 0.004 | 0.001 | 0.004 | |
| getCondMsg | 0.000 | 0.000 | 0.001 | |
| getConditionSelector | 0.001 | 0.000 | 0.001 | |
| getConditionSelectorFromMeta | 0.004 | 0.000 | 0.005 | |
| getCutOffSelection | 0.002 | 0.000 | 0.002 | |
| getDEAnalysisText | 0.003 | 0.000 | 0.003 | |
| getDEResultsUI | 0.002 | 0.000 | 0.002 | |
| getDataAssesmentText | 0.003 | 0.000 | 0.003 | |
| getDataForTables | 0.001 | 0.001 | 0.001 | |
| getDataPreparationText | 0.001 | 0.000 | 0.002 | |
| getDensityPlot | 0.000 | 0.000 | 0.001 | |
| getDensityPlotUI | 0.001 | 0.000 | 0.001 | |
| getDomains | 0.000 | 0.000 | 0.001 | |
| getDown | 0.000 | 0.001 | 0.000 | |
| getDownloadSection | 0.012 | 0.000 | 0.012 | |
| getEnrichDO | 0.000 | 0.000 | 0.001 | |
| getEnrichGO | 0 | 0 | 0 | |
| getEnrichKEGG | 0.001 | 0.000 | 0.001 | |
| getEntrezIds | 0 | 0 | 0 | |
| getEntrezTable | 0.000 | 0.000 | 0.001 | |
| getGOLeftMenu | 0.012 | 0.001 | 0.011 | |
| getGOPlots | 0.000 | 0.000 | 0.001 | |
| getGeneList | 0.844 | 0.085 | 0.929 | |
| getGeneSetData | 0.001 | 0.000 | 0.001 | |
| getGoPanel | 0.036 | 0.005 | 0.041 | |
| getHeatmapUI | 0.001 | 0.000 | 0.001 | |
| getHelpButton | 0 | 0 | 0 | |
| getHideLegendOnOff | 0.005 | 0.001 | 0.005 | |
| getHistogramUI | 0.000 | 0.000 | 0.001 | |
| getIQRPlot | 0.001 | 0.000 | 0.001 | |
| getIQRPlotUI | 0 | 0 | 0 | |
| getIntroText | 0.002 | 0.000 | 0.002 | |
| getJSLine | 0.004 | 0.000 | 0.004 | |
| getKEGGModal | 0.004 | 0.000 | 0.005 | |
| getLeftMenu | 0.001 | 0.000 | 0.001 | |
| getLegendColors | 0.001 | 0.001 | 0.002 | |
| getLegendRadio | 0.004 | 0.000 | 0.004 | |
| getLegendSelect | 0.004 | 0.000 | 0.004 | |
| getLevelOrder | 0.000 | 0.000 | 0.001 | |
| getLoadingMsg | 0.003 | 0.001 | 0.003 | |
| getLogo | 0.002 | 0.000 | 0.002 | |
| getMainPanel | 0.002 | 0.001 | 0.002 | |
| getMainPlotUI | 0.001 | 0.000 | 0.000 | |
| getMainPlotsLeftMenu | 0.091 | 0.002 | 0.094 | |
| getMean | 0.000 | 0.000 | 0.001 | |
| getMergedComparison | 0.001 | 0.000 | 0.001 | |
| getMetaSelector | 0.001 | 0.000 | 0.000 | |
| getMethodDetails | 0.001 | 0.000 | 0.001 | |
| getMostVariedList | 0.000 | 0.000 | 0.001 | |
| getNormalizedMatrix | 0.077 | 0.003 | 0.079 | |
| getOrganism | 0.001 | 0.001 | 0.001 | |
| getOrganismBox | 0.004 | 0.001 | 0.005 | |
| getOrganismPathway | 0.001 | 0.000 | 0.001 | |
| getPCAPlotUI | 0.000 | 0.000 | 0.001 | |
| getPCAcontolUpdatesJS | 0.001 | 0.000 | 0.001 | |
| getPCAexplained | 2.672 | 0.080 | 2.754 | |
| getPCselection | 0.001 | 0.000 | 0.001 | |
| getPlotArea | 0 | 0 | 0 | |
| getProgramTitle | 0 | 0 | 0 | |
| getQAText | 0.003 | 0.000 | 0.002 | |
| getQCLeftMenu | 0.000 | 0.001 | 0.001 | |
| getQCPanel | 0.006 | 0.001 | 0.006 | |
| getSampleDetails | 0.000 | 0.000 | 0.001 | |
| getSampleNames | 0.001 | 0.000 | 0.001 | |
| getSamples | 0 | 0 | 0 | |
| getSearchData | 0.001 | 0.000 | 0.000 | |
| getSelHeat | 0.001 | 0.001 | 0.000 | |
| getSelectInputBox | 0.000 | 0.001 | 0.001 | |
| getSelectedCols | 0.001 | 0.001 | 0.001 | |
| getSelectedDatasetInput | 0 | 0 | 0 | |
| getShapeColor | 0.001 | 0.000 | 0.001 | |
| getStartPlotsMsg | 0.004 | 0.000 | 0.004 | |
| getStartupMsg | 0.004 | 0.000 | 0.004 | |
| getTabUpdateJS | 0 | 0 | 0 | |
| getTableDetails | 0.001 | 0.000 | 0.001 | |
| getTableModal | 0.014 | 0.002 | 0.015 | |
| getTableStyle | 0.001 | 0.000 | 0.000 | |
| getTextOnOff | 0.003 | 0.001 | 0.004 | |
| getUp | 0.001 | 0.001 | 0.000 | |
| getUpDown | 0 | 0 | 0 | |
| getVariationData | 0 | 0 | 0 | |
| get_conditions_given_selection | 0.001 | 0.001 | 0.001 | |
| heatmapControlsUI | 0.064 | 0.003 | 0.066 | |
| heatmapJScode | 0.000 | 0.001 | 0.001 | |
| heatmapServer | 0.001 | 0.000 | 0.002 | |
| heatmapUI | 0.104 | 0.005 | 0.108 | |
| hideObj | 0.001 | 0.000 | 0.001 | |
| histogramControlsUI | 0.001 | 0.001 | 0.000 | |
| installpack | 0.001 | 0.000 | 0.001 | |
| kmeansControlsUI | 0.005 | 0.000 | 0.005 | |
| lcfMetRadio | 0.003 | 0.000 | 0.003 | |
| loadpack | 0.015 | 0.030 | 0.045 | |
| mainPlotControlsUI | 0.005 | 0.000 | 0.005 | |
| mainScatterNew | 0.001 | 0.000 | 0.001 | |
| niceKmeans | 0 | 0 | 0 | |
| normalizationMethods | 0.003 | 0.000 | 0.004 | |
| palUI | 0.004 | 0.001 | 0.005 | |
| panel.cor | 0.001 | 0.000 | 0.001 | |
| panel.hist | 0.001 | 0.001 | 0.001 | |
| pcaPlotControlsUI | 0.011 | 0.000 | 0.011 | |
| plotData | 0.000 | 0.001 | 0.000 | |
| plotMarginsUI | 0.005 | 0.000 | 0.005 | |
| plotSizeMarginsUI | 0.009 | 0.000 | 0.009 | |
| plotSizeUI | 0.002 | 0.000 | 0.002 | |
| plotTypeUI | 0.001 | 0.000 | 0.001 | |
| plot_pca | 1.477 | 0.066 | 1.552 | |
| prepDEOutput | 0.001 | 0.000 | 0.001 | |
| prepDataContainer | 0.001 | 0.000 | 0.001 | |
| prepGroup | 0 | 0 | 0 | |
| prepHeatData | 0.001 | 0.000 | 0.001 | |
| prepPCADat | 0.000 | 0.001 | 0.001 | |
| push | 0.000 | 0.001 | 0.001 | |
| removeCols | 0.001 | 0.000 | 0.000 | |
| removeExtraCols | 0.002 | 0.000 | 0.002 | |
| round_vals | 0.000 | 0.000 | 0.001 | |
| runDE | 0.001 | 0.000 | 0.001 | |
| runDESeq2 | 0.000 | 0.001 | 0.001 | |
| runEdgeR | 0.001 | 0.001 | 0.001 | |
| runHeatmap | 0.001 | 0.000 | 0.001 | |
| runHeatmap2 | 0.001 | 0.000 | 0.001 | |
| runLimma | 0.001 | 0.001 | 0.001 | |
| run_pca | 1.309 | 0.035 | 1.346 | |
| selectConditions | 0.001 | 0.000 | 0.001 | |
| selectGroupInfo | 0.001 | 0.000 | 0.000 | |
| selectedInput | 0.000 | 0.001 | 0.001 | |
| sepRadio | 0.004 | 0.000 | 0.004 | |
| setBatch | 0 | 0 | 0 | |
| showObj | 0.001 | 0.000 | 0.000 | |
| startDEBrowser | 0.000 | 0.001 | 0.000 | |
| startHeatmap | 0.000 | 0.000 | 0.001 | |
| textareaInput | 0 | 0 | 0 | |
| togglePanels | 0 | 0 | 0 | |