Alper Kucukural
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/debrowser |
| Branch: RELEASE_3_6 |
| Last Commit: b90f280 |
| Last Changed Date: 2017-12-04 11:24:56 -0400 (Mon, 04 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:42:33 -0400 (Thu, 12 Apr 2018).
| Package 338/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| debrowser 1.6.8 Alper Kucukural
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: debrowser |
| Version: 1.6.8 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_1.6.8.tar.gz |
| StartedAt: 2018-04-12 02:35:08 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:41:09 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 360.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: debrowser.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_1.6.8.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/debrowser.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.8’
* 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 ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
doc 6.2Mb
extdata 2.1Mb
* 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 loading without being on the library search path ... 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
MAPlot: no visible global function definition for ‘:=’
MAPlot: no visible binding for global variable ‘size’
MAPlot: no visible binding for global variable ‘size.hover’
MAPlot: no visible binding for global variable ‘fillOpacity’
MAPlot: no visible binding for global variable ‘fillOpacity.hover’
MAPlot: no visible binding for global variable ‘fill.brush’
MAPlot: no visible binding for global variable ‘opacity’
MAPlot: no visible binding for global variable ‘key’
MAZoom: no visible global function definition for ‘:=’
MAZoom: no visible binding for global variable ‘size’
MAZoom: no visible binding for global variable ‘size.hover’
MAZoom: no visible binding for global variable ‘key’
bookmarkServer: no visible binding for global variable ‘NUL’
deServer: no visible binding for global variable ‘debrowser’
deServer: no visible global function definition for ‘renderImage’
getDensityPlot: no visible binding for global variable ‘samples’
getHoverPlots: no visible binding for global variable ‘conds’
getIQRPlot: no visible global function definition for ‘:=’
getIQRPlot: no visible binding for global variable ‘fill’
getKEGGModal: no visible global function definition for ‘div’
getKEGGModal: no visible global function definition for ‘imageOutput’
getSelectedDatasetInput: no visible binding for global variable
‘searched’
installpack: no visible global function definition for ‘biocLite’
load_data: no visible binding for global variable ‘demodata’
mainScatter: no visible global function definition for ‘:=’
mainScatter: no visible binding for global variable ‘size’
mainScatter: no visible binding for global variable ‘size.hover’
mainScatter: no visible binding for global variable ‘fillOpacity’
mainScatter: no visible binding for global variable ‘fillOpacity.hover’
mainScatter: no visible binding for global variable ‘fill.brush’
mainScatter: no visible binding for global variable ‘opacity’
mainScatter: no visible binding for global variable ‘key’
plot_pca: no visible global function definition for ‘:=’
plot_pca: no visible binding for global variable ‘key’
plot_pca: no visible binding for global variable ‘fontSize’
plot_pca: no visible binding for global variable ‘align’
plot_pca: no visible binding for global variable ‘baseline’
plot_pca: no visible binding for global variable ‘stroke’
runBayseq: no visible binding for global variable ‘fit’
scatterZoom: no visible global function definition for ‘:=’
scatterZoom: no visible binding for global variable ‘size’
scatterZoom: no visible binding for global variable ‘size.hover’
scatterZoom: no visible binding for global variable ‘key’
startDEBrowser: no visible binding for global variable
‘.startdebrowser.called’
volcanoPlot: no visible global function definition for ‘:=’
volcanoPlot: no visible binding for global variable ‘size’
volcanoPlot: no visible binding for global variable ‘size.hover’
volcanoPlot: no visible binding for global variable ‘fillOpacity’
volcanoPlot: no visible binding for global variable ‘fillOpacity.hover’
volcanoPlot: no visible binding for global variable ‘fill.brush’
volcanoPlot: no visible binding for global variable ‘opacity’
volcanoPlot: no visible binding for global variable ‘key’
volcanoZoom: no visible global function definition for ‘:=’
volcanoZoom: no visible binding for global variable ‘size’
volcanoZoom: no visible binding for global variable ‘size.hover’
volcanoZoom: no visible binding for global variable ‘key’
Undefined global functions or variables:
.startdebrowser.called := NUL align baseline biocLite conds debrowser
demodata div fill fill.brush fillOpacity fillOpacity.hover fit
fontSize imageOutput key opacity renderImage samples searched size
size.hover stroke
* 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 installed files from ‘inst/doc’ ... 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/debrowser.Rcheck/00check.log’
for details.
debrowser.Rcheck/00install.out
* installing *source* package ‘debrowser’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (debrowser)
debrowser.Rcheck/tests/test-demo.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Loading required package: ggvis
Loading required package: jsonlite
Attaching package: 'jsonlite'
The following object is masked from 'package:shiny':
validate
Loading required package: shinyjs
Attaching package: 'shinyjs'
The following object is masked from 'package:shiny':
runExample
The following objects are masked from 'package:methods':
removeClass, show
##############################################################################
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).
##############################################################################
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> 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, 3], 7.1)
+ expect_equal(demodata[29311, 6], 2)
+ expect_equal(demodata[29311, 7], 6)
+ expect_null(demodata[1, 8])
+ })
>
> proc.time()
user system elapsed
11.488 0.446 12.135
debrowser.Rcheck/tests/test-deseq.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Loading required package: shiny
Loading required package: ggvis
Loading required package: jsonlite
Attaching package: 'jsonlite'
The following object is masked from 'package:shiny':
validate
Loading required package: shinyjs
Attaching package: 'shinyjs'
The following object is masked from 'package:shiny':
runExample
The following objects are masked from 'package:methods':
removeClass, show
##############################################################################
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).
##############################################################################
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
> library(edgeR)
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:DESeq2':
plotMA
The following object is masked from 'package:BiocGenerics':
plotMA
> 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])
>
> test_that("Able to run DESeq2", {
+ deseqrun <- runDESeq(data, columns, conds)
+ expect_true(exists("deseqrun"))
+ })
>
> test_that("Linked brush initialization", {
+ expect_silent( lb <- linked_brush())
+ expect_true(exists("lb"))
+ })
>
> ##################################################
> deseqrun <- runDESeq(data, columns, conds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> lb <- linked_brush()
>
> 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) )
+
+ heatmap <- runHeatmap(mtcars)
+ expect_false( is.null(heatmap) )
+ expect_silent( MAP <- MAPlot(dat, lb) )
+ expect_false( is.null(MAP) )
+
+ expect_silent( test_scat <- mainScatter(rdata, lb,
+ x="Cond1", y="Cond2") )
+ expect_false(is.null(test_scat))
+ expect_silent( test_scat_zoom <- scatterZoom(rdata,
+ x="Cond1", y="Cond2") )
+ expect_false(is.null(test_scat_zoom))
+
+ expect_silent( test_volc <- volcanoPlot(rdata, lb) )
+ expect_false(is.null(test_volc))
+ expect_silent( test_volc_zoom <- volcanoZoom(rdata) )
+ expect_false(is.null(test_volc_zoom))
+
+ expect_silent( test_ma <- MAPlot(dat, lb) )
+ expect_false(is.null(test_ma))
+ expect_silent( test_ma_zoom <- MAZoom(dat) )
+ expect_false(is.null(test_ma_zoom))
+ })
>
>
> proc.time()
user system elapsed
37.336 0.790 38.918
debrowser.Rcheck/tests/test-null.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Loading required package: ggvis
Loading required package: jsonlite
Attaching package: 'jsonlite'
The following object is masked from 'package:shiny':
validate
Loading required package: shinyjs
Attaching package: 'shinyjs'
The following object is masked from 'package:shiny':
runExample
The following objects are masked from 'package:methods':
removeClass, show
##############################################################################
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).
##############################################################################
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> library(testthat)
>
> test_that("passing no data returns NULL", {
+ expect_null(getSampleNames(NULL))
+ expect_null(compareClust() )
+ expect_null(getGOPlots(NULL, NULL))
+ null_deseq <- runDESeq(NULL)
+ expect_null(null_deseq)
+ expect_null(mainScatter(NULL))
+ expect_null(scatterZoom(NULL))
+ expect_null(MAPlot(NULL))
+ expect_null(MAZoom(NULL))
+ expect_null(volcanoPlot(NULL))
+ expect_null(volcanoZoom(NULL))
+ expect_null(plot_pca(NULL))
+ })
>
> proc.time()
user system elapsed
10.396 0.410 10.915
debrowser.Rcheck/tests/test-ui.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Loading required package: ggvis
Loading required package: jsonlite
Attaching package: 'jsonlite'
The following object is masked from 'package:shiny':
validate
Loading required package: shinyjs
Attaching package: 'shinyjs'
The following object is masked from 'package:shiny':
runExample
The following objects are masked from 'package:methods':
removeClass, show
##############################################################################
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).
##############################################################################
Attaching package: 'debrowser'
The following object is masked from 'package:shiny':
actionButton
> library(testthat)
>
> test_that("able to create the basic UI", {
+ expect_silent( getDataPrep <- getDataPrepPanel(TRUE) )
+ expect_true(exists("getDataPrep"))
+ expect_equal(getDataPrep[[1]][[1]],"div")
+ })
>
> 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(TRUE) )
+ expect_true(exists("downloads"))
+ expect_equal(downloads[[1]][[1]], "div")
+
+ expect_silent( getMain <- getMainPanel("randstr") )
+ 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
11.251 0.422 11.864
debrowser.Rcheck/debrowser-Ex.timings
| name | user | system | elapsed | |
| MAPlot | 0.001 | 0.000 | 0.000 | |
| MAZoom | 0.000 | 0.000 | 0.001 | |
| actionButton | 0.068 | 0.001 | 0.072 | |
| addDataCols | 0.001 | 0.000 | 0.001 | |
| addID | 0.001 | 0.000 | 0.001 | |
| add_title_pos | 1.291 | 0.032 | 1.348 | |
| all2all | 0.156 | 0.009 | 0.166 | |
| applyFilters | 0.001 | 0.000 | 0.001 | |
| applyFiltersToMergedComparison | 0.000 | 0.000 | 0.001 | |
| bookmarkServer | 0.001 | 0.000 | 0.001 | |
| bookmarkUI | 0.000 | 0.000 | 0.001 | |
| clusterData | 0.001 | 0.000 | 0.001 | |
| compareClust | 0.001 | 0.000 | 0.001 | |
| copy2newDirectory | 0.001 | 0.000 | 0.001 | |
| correctBatchEffect | 0.001 | 0.000 | 0.001 | |
| deServer | 0.016 | 0.002 | 0.018 | |
| deUI | 0.265 | 0.007 | 0.291 | |
| drawPCAExplained | 0.000 | 0.000 | 0.001 | |
| getAfterLoadMsg | 0.001 | 0.000 | 0.001 | |
| getColorShapeSelection | 0.000 | 0.000 | 0.001 | |
| getColors | 0.000 | 0.000 | 0.001 | |
| getCompSelection | 0.028 | 0.001 | 0.029 | |
| getCondMsg | 0.001 | 0.000 | 0.001 | |
| getConditionSelector | 0.000 | 0.000 | 0.001 | |
| getConditionSelectorFromMeta | 0.000 | 0.000 | 0.001 | |
| getCutOffSelection | 0.091 | 0.001 | 0.092 | |
| getDataForTables | 0.001 | 0.001 | 0.001 | |
| getDataPrepPanel | 0.001 | 0.000 | 0.000 | |
| getDensityPlot | 0.001 | 0.000 | 0.001 | |
| getDomains | 0.000 | 0.000 | 0.001 | |
| getDown | 0.001 | 0.000 | 0.001 | |
| getDownloadSection | 0.001 | 0.000 | 0.001 | |
| getEnrichDO | 0.001 | 0.000 | 0.001 | |
| getEnrichGO | 0.001 | 0.000 | 0.001 | |
| getEnrichKEGG | 0 | 0 | 0 | |
| getEntrezIds | 0.001 | 0.000 | 0.001 | |
| getGOLeftMenu | 0.100 | 0.002 | 0.105 | |
| getGOPlots | 0.000 | 0.001 | 0.000 | |
| getGeneList | 0.767 | 0.037 | 0.810 | |
| getGeneSetData | 0.001 | 0.000 | 0.001 | |
| getGoPanel | 0.044 | 0.002 | 0.046 | |
| getHelpButton | 0.001 | 0.000 | 0.001 | |
| getHoverPlots | 0.001 | 0.000 | 0.000 | |
| getIQRPlot | 0.000 | 0.001 | 0.000 | |
| getInitialMenu | 0.001 | 0.000 | 0.001 | |
| getIntHeatmap | 0.001 | 0.000 | 0.001 | |
| getIntHeatmapVis | 0.001 | 0.000 | 0.001 | |
| getJsonObj | 0.001 | 0.000 | 0.001 | |
| getKEGGModal | 0.043 | 0.000 | 0.043 | |
| getLeftMenu | 0.001 | 0.000 | 0.001 | |
| getLegendSelect | 0.004 | 0.000 | 0.005 | |
| getLoadingMsg | 0.002 | 0.000 | 0.002 | |
| getLogo | 0.001 | 0.000 | 0.002 | |
| getMainPanel | 0.001 | 0.000 | 0.001 | |
| getMainPanelPlots | 0.002 | 0.000 | 0.001 | |
| getMainPlotsLeftMenu | 0.002 | 0.000 | 0.002 | |
| getMean | 0.000 | 0.001 | 0.000 | |
| getMergedComparison | 0.000 | 0.000 | 0.001 | |
| getMethodDetails | 0.001 | 0.000 | 0.001 | |
| getMostVariedList | 0.000 | 0.000 | 0.001 | |
| getNormalizedMatrix | 0.060 | 0.000 | 0.059 | |
| getOrganism | 0.001 | 0.000 | 0.001 | |
| getOrganismBox | 0.003 | 0.000 | 0.004 | |
| getOrganismPathway | 0.001 | 0.000 | 0.001 | |
| getPCAexplained | 1.765 | 0.060 | 1.845 | |
| getPCselection | 0.011 | 0.001 | 0.011 | |
| getProgramTitle | 0.001 | 0.000 | 0.004 | |
| getQCLeftMenu | 0.001 | 0.001 | 0.001 | |
| getQCPanel | 0.037 | 0.002 | 0.039 | |
| getQCPlots | 0.001 | 0.000 | 0.001 | |
| getQCReplot | 0.001 | 0.001 | 0.001 | |
| getSampleNames | 0.001 | 0.000 | 0.001 | |
| getSamples | 0.001 | 0.000 | 0.000 | |
| getSearchData | 0.001 | 0.000 | 0.001 | |
| getSelHeat | 0.001 | 0.000 | 0.001 | |
| getSelectInputBox | 0.001 | 0.000 | 0.001 | |
| getSelectedCols | 0.001 | 0.001 | 0.001 | |
| getSelectedDatasetInput | 0.001 | 0.000 | 0.000 | |
| getShapeColor | 0.001 | 0.000 | 0.000 | |
| getStartPlotsMsg | 0.003 | 0.001 | 0.003 | |
| getStartupMsg | 0.003 | 0.001 | 0.004 | |
| getTableStyle | 0.000 | 0.000 | 0.001 | |
| getTextOnOff | 0.003 | 0.001 | 0.005 | |
| getToolTipPCA | 0 | 0 | 0 | |
| getToolTipText | 0.001 | 0.000 | 0.001 | |
| getUp | 0.000 | 0.000 | 0.001 | |
| getUpDown | 0.000 | 0.000 | 0.001 | |
| get_state_id | 0.001 | 0.000 | 0.001 | |
| get_user_info | 0.001 | 0.000 | 0.001 | |
| hideObj | 0.001 | 0.000 | 0.000 | |
| installpack | 0.001 | 0.000 | 0.001 | |
| link_brush | 0.005 | 0.000 | 0.005 | |
| load_data | 0.001 | 0.000 | 0.001 | |
| loadpack | 0.011 | 0.009 | 0.020 | |
| logSliderJScode | 0.000 | 0.000 | 0.001 | |
| mainScatter | 0.001 | 0.000 | 0.001 | |
| panel.cor | 0.001 | 0.000 | 0.001 | |
| panel.hist | 0.001 | 0.000 | 0.001 | |
| plot_pca | 1.095 | 0.035 | 1.158 | |
| prepAddQCPlots | 0.001 | 0.000 | 0.001 | |
| prepDEOutput | 0.001 | 0.000 | 0.001 | |
| prepDataContainer | 0.001 | 0.000 | 0.001 | |
| prepDataForQC | 0.001 | 0.000 | 0.001 | |
| push | 0.001 | 0.000 | 0.001 | |
| readMetaData | 0.001 | 0.000 | 0.000 | |
| removeBookmark | 0.001 | 0.000 | 0.001 | |
| removeCols | 0.001 | 0.000 | 0.001 | |
| round_vals | 0.001 | 0.000 | 0.001 | |
| runBayseq | 0.001 | 0.001 | 0.001 | |
| runDE | 0.001 | 0.000 | 0.001 | |
| runDESeq | 0.001 | 0.000 | 0.001 | |
| runDESeq2 | 0.000 | 0.000 | 0.001 | |
| runEdgeR | 0.001 | 0.000 | 0.001 | |
| runHeatmap | 0.363 | 0.004 | 0.367 | |
| runLimma | 0.000 | 0.001 | 0.000 | |
| run_pca | 1.002 | 0.038 | 1.065 | |
| saveQCPlot | 0.001 | 0.000 | 0.001 | |
| scatterZoom | 0.001 | 0.000 | 0.000 | |
| selectBatchEffect | 0.001 | 0.000 | 0.000 | |
| selectConditions | 0.001 | 0.000 | 0.001 | |
| selectedInput | 0.001 | 0.000 | 0.000 | |
| setFilterParams | 0.000 | 0.000 | 0.001 | |
| showObj | 0 | 0 | 0 | |
| startDEBrowser | 0.001 | 0.000 | 0.001 | |
| textareaInput | 0.001 | 0.001 | 0.001 | |
| togglePanels | 0.001 | 0.000 | 0.001 | |
| volcanoPlot | 0.000 | 0.000 | 0.001 | |
| volcanoZoom | 0.001 | 0.001 | 0.001 | |
| whitelist | 0.001 | 0.000 | 0.001 | |