scater

Package: scater
Type: Package
Maintainer: Davis McCarthy <davis@ebi.ac.uk>
Author: Davis McCarthy
Authors@R: c(person("Davis", "McCarthy", role=c("aut", "cre"),
email="davis@ebi.ac.uk"), person("Quin", "Wills",
role=c("aut"), email="qilin@quinwills.net"), person("Kieran",
"Campbell", role=c("aut"),
email="kieran.campbell@sjc.ox.ac.uk"), person("Vladimir",
"Kiselev", role=c("ctb"),
email="vk6@sanger.ac.uk"))
Version: 1.0.4
Date: 2016-05-19
License: GPL (>= 2)
Title: Single-cell analysis toolkit for gene expression data in R
Description: A collection of tools for doing various analyses of
single-cell RNA-seq gene expression data, with a focus on
quality control.
Depends: R (>= 3.3), Biobase, ggplot2, methods
Imports: biomaRt, BiocGenerics, data.table, dplyr, edgeR, grid, limma,
matrixStats, parallel, plyr, reshape2, rhdf5, rjson, shiny,
shinydashboard, tximport, viridis
Suggests: BiocStyle, cowplot, cluster, destiny, knitr, monocle,
mvoutlier, rmarkdown, Rtsne, testthat, magrittr
VignetteBuilder: knitr
LazyData: true
biocViews: RNASeq, QualityControl, Preprocessing, Normalization,
Visualization, DimensionReduction, Transcriptomics,
GeneExpression, Sequencing, Software, DataImport,
DataRepresentation, Infrastructure
RoxygenNote: 5.0.1
NeedsCompilation: no
URL: https://github.com/davismcc/scater
BugReports: https://github.com/davismcc/scater/issues
Packaged: 2016-06-13 05:48:39 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'scater' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for 'mutate' in package 'scater'
Creating a new generic function for 'filter' in package 'scater'
Creating a generic function for 'plot' from package 'graphics' in package 'scater'
** help
*** installing help indices
  converting help for package 'scater'
    finding HTML links ... done
    SCESet-subset                           html  
Rd warning: /tmp/RtmpTZaQh2/R.INSTALL31d12f2105f5/scater/man/SCESet-subset.Rd:21: missing file link 'as.integer'
    SCESet                                  html  
    arrange                                 html  
    bootstraps                              html  
    calcIsExprs                             html  
    calculateFPKM                           html  
    calculateQCMetrics                      html  
    calculateTPM                            html  
    cellNames                               html  
Rd warning: /tmp/RtmpTZaQh2/R.INSTALL31d12f2105f5/scater/man/cellNames.Rd:19: missing file link 'sampleNames'
    cellPairwiseDistances                   html  
    counts                                  html  
    cpm                                     html  
    fData                                   html  
    featurePairwiseDistances                html  
    filter                                  html  
    findImportantPCs                        html  
    finding level-2 HTML links ... done

    fpkm                                    html  
    fromCellDataSet                         html  
    getBMFeatureAnnos                       html  
    getExprs                                html  
    get_exprs                               html  
    isOutlier                               html  
    is_exprs                                html  
    multiplot                               html  
    mutate                                  html  
    newSCESet                               html  
    norm_counts                             html  
    norm_cpm                                html  
    norm_exprs                              html  
    norm_fpkm                               html  
    norm_tpm                                html  
    normaliseExprs                          html  
    normalize                               html  
    pData                                   html  
    plot                                    html  
    plotDiffusionMap                        html  
Rd warning: /tmp/RtmpTZaQh2/R.INSTALL31d12f2105f5/scater/man/plotDiffusionMap.Rd:29: missing file link 'DiffusionMap'
Rd warning: /tmp/RtmpTZaQh2/R.INSTALL31d12f2105f5/scater/man/plotDiffusionMap.Rd:87: missing file link 'DiffusionMap'
Rd warning: /tmp/RtmpTZaQh2/R.INSTALL31d12f2105f5/scater/man/plotDiffusionMap.Rd:89: missing file link 'DiffusionMap'
Rd warning: /tmp/RtmpTZaQh2/R.INSTALL31d12f2105f5/scater/man/plotDiffusionMap.Rd:103: missing file link 'DiffusionMap'
    plotExplanatoryVariables                html  
    plotExpression                          html  
    plotExprsFreqVsMean                     html  
    plotFeatureData                         html  
    plotHighestExprs                        html  
    plotMDS                                 html  
    plotMetadata                            html  
    plotPCA                                 html  
    plotPhenoData                           html  
    plotQC                                  html  
    plotReducedDim                          html  
    plotTSNE                                html  
    readKallistoResults                     html  
    readKallistoResultsOneSample            html  
    readSalmonResults                       html  
    readSalmonResultsOneSample              html  
    readTxResults                           html  
    reducedDimension                        html  
    rename                                  html  
    runKallisto                             html  
    sc_example_cell_info                    html  
    sc_example_counts                       html  
    scater-package                          html  
    scater_gui                              html  
    set_exprs                               html  
    sizeFactors                             html  
    stand_exprs                             html  
    summariseExprsAcrossFeatures            html  
    toCellDataSet                           html  
    tpm                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scater)
Making 'packages.html' ... done