debrowser

Package: debrowser
Type: Package
Title: debrowser: Interactive Differential Expresion Analysis Browser
Version: 1.0.4
Date: 2016-05-05
Author: Alper Kucukural <alper.kucukural@umassmed.edu>,
Nicholas Merowsky <nicholas.merowsky@umassmed.edu>,
Manuel Garber <manuel.garber@umassmed.edu>
Maintainer: Alper Kucukural <alper.kucukural@umassmed.edu>
Description: Bioinformatics platform containing interactive plots and tables
for differential gene and region expression studies. Allows visualizing
expression data much more deeply in an interactive and faster way. By
changing the parameters, user can easily discover different parts of the
data that like never have been done before. Manually creating and looking
these plots takes time. With this system users can prepare plots without
writing any code. Differential expression, PCA and clustering analysis are
made on site and the results are shown in various plots such as scatter,
bar, box, volcano, ma plots and Heatmaps.
Depends: R (>= 3.3.0), shiny, ggvis, jsonlite, edgeR, shinyjs
License: GPL-3 + file LICENSE
LazyData: true
Imports: clusterProfiler, DT, ReactomePA, ggplot2, RColorBrewer,
annotate, gplots, AnnotationDbi, DESeq2, DOSE, igraph,
grDevices, graphics, stats, utils, GenomicRanges, IRanges,
S4Vectors, SummarizedExperiment, stringi, reshape2,
org.Hs.eg.db, org.Mm.eg.db
RoxygenNote: 5.0.1
Suggests: testthat, rmarkdown, knitr, R.rsp
VignetteBuilder: knitr, R.rsp
URL: https://github.com/UMMS-Biocore/debrowser
BugReports: https://github.com/UMMS-Biocore/debrowser/issues/new
biocViews: Sequencing, ChIPSeq, RNASeq, DifferentialExpression,
GeneExpression, Clustering
NeedsCompilation: no
Packaged: 2016-05-16 06:03:02 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'debrowser' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'debrowser'
    finding HTML links ... done
    MAPlot                                  html  
    MAZoom                                  html  
    addID                                   html  
    add_title_pos                           html  
    all2all                                 html  
    applyFilters                            html  
    applyFiltersToMergedComparison          html  
    cellInfo                                html  
    clusterData                             html  
    compareClust                            html  
    deServer                                html  
    deUI                                    html  
    getAfterLoadMsg                         html  
    getColors                               html  
    getCompSelection                        html  
    getCondMsg                              html  
    getConditionSelector                    html  
    getCutOffSelection                      html  
    getDataForTables                        html  
    getDataPrepPanel                        html  
    getDomains                              html  
    getDown                                 html  
    getDownloadSection                      html  
    getEnrichDO                             html  
    getEnrichGO                             html  
    getEnrichKEGG                           html  
    getGOLeftMenu                           html  
    getGOPlots                              html  
    getGeneList                             html  
    getGeneSetData                          html  
    getGoPanel                              html  
    getHoverPlots                           html  
    getInitialMenu                          html  
    getIntHeatmap                           html  
    getIntHeatmapVis                        html  
    getLeftMenu                             html  
    getLoadingMsg                           html  
    getLogo                                 html  
    getMainPanel                            html  
    getMainPanelPlots                       html  
    getMean                                 html  
    getMergedComparison                     html  
    getMostVariedList                       html  
    getNormalizedMatrix                     html  
    getOrganism                             html  
    getOrganismBox                          html  
    getOrganismPathway                      html  
    getPCAexplained                         html  
    getPCselection                          html  
    getProgramTitle                         html  
    getQCLeftMenu                           html  
    getQCPanel                              html  
    getQCPlots                              html  
    getQCReplot                             html  
    getSampleNames                          html  
    getSamples                              html  
    getSearchData                           html  
    getSelHeat                              html  
    getSelectedDatasetInput                 html  
    getStartPlotsMsg                        html  
    getStartupMsg                           html  
    getTableStyle                           html  
    getToolTipText                          html  
    getUp                                   html  
    getUpDown                               html  
    hideObj                                 html  
    installpack                             html  
    link_brush                              html  
    load_data                               html  
    logSliderJScode                         html  
    mainScatter                             html  
    panel.cor                               html  
    panel.hist                              html  
    plot_pca                                html  
    prepDESeqOutput                         html  
    prepDataContainer                       html  
    prepDataForQC                           html  
    push                                    html  
    removeCols                              html  
    round_vals                              html  
    runDESeq                                html  
    runHeatmap                              html  
    run_pca                                 html  
    saveQCPlot                              html  
    scatterZoom                             html  
    selectConditions                        html  
    setFilterParams                         html  
    showObj                                 html  
    startDEBrowser                          html  
    textareaInput                           html  
    togglePanels                            html  
    volcanoPlot                             html  
    volcanoZoom                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (debrowser)
Making 'packages.html' ... done