TCGAbiolinks

Package: TCGAbiolinks
Type: Package
Title: TCGAbiolinks: An R/Bioconductor package for integrative analysis
with TCGA data
Version: 1.2.5
Date: 2015-12-13
Author: Antonio Colaprico,
Tiago Chedraoui Silva,
Catharina Olsen,
Luciano Garofano,
Davide Garolini,
Claudia Cava,
Thais Sabedot,
Tathiane Malta,
Stefano M. Pagnotta,
Isabella Castiglioni,
Michele Ceccarelli,
Gianluca Bontempi,
Houtan Noushmehr
Maintainer: Antonio Colaprico <antonio.colaprico@ulb.ac.be>,
Tiago Chedraoui Silva <tiagochst@usp.br>
Depends: R (>= 3.2)
Imports: downloader (>= 0.4), GGally, grDevices, graphics,
GenomicRanges, XML, Biobase, affy, xtable, data.table, EDASeq
(>= 2.0.0), RCurl, edgeR (>= 3.0.0), rjson, plyr, knitr,
biomaRt, coin, gplots, ggplot2, ggthemes, survival, stringr (>=
1.0.0), IRanges, scales, rvest (>= 0.3.0), stats, utils, dnet,
igraph, supraHex, S4Vectors, SummarizedExperiment,
BiocGenerics, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene, limma, genefilter,
ConsensusClusterPlus, RColorBrewer, doParallel, dplyr,
parallel, xml2, sjPlot (>= 2.0), magrittr, cowplot, reshape2,
gtable, sjmisc, httr, matlab, circlize, ComplexHeatmap, ggrepel
Description: The aim of TCGAbiolinks is : i) facilitate the TCGA open-access
data retrieval, ii) prepare the data using the appropriate pre-processing
strategies, iii) provide the means to carry out different standard analyses
and iv) allow the user to download a specific version of the data and thus
to easily reproduce earlier research results. In more detail, the package
provides multiple methods for analysis (e.g., differential expression analysis,
identifying differentially methylated regions) and methods for visualization
(e.g., survival plots, volcano plots, starburst plots) in order to easily
develop complete analysis pipelines.
License: GPL (>= 3)
biocViews: DNAMethylation, DifferentialMethylation, GeneRegulation,
GeneExpression, MethylationArray, DifferentialExpression,
Pathways, Network, Survival
Suggests: testthat, png, BiocStyle, rmarkdown, devtools
VignetteBuilder: knitr
LazyData: true
URL: https://github.com/BioinformaticsFMRP/TCGAbiolinks
BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-07 05:36:21 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TCGAbiolinks'
    finding HTML links ... done
    BRCA_RNASeqV2_version                   html  
    BRCA_rnaseqv2                           html  
    ER_status_BRCA                          html  
    GeneSplitRegulon                        html  
    GenesCutID                              html  
    HER_status_BRCA                         html  
    PR_status_BRCA                          html  
    TCGAUpdate                              html  
    TCGAVisualize_volcano                   html  
    TCGAanalyze_Clustering                  html  
    TCGAanalyze_DEA                         html  
    TCGAanalyze_DEA_Affy                    html  
    TCGAanalyze_DMR                         html  
    TCGAanalyze_EA                          html  
    TCGAanalyze_EAcomplete                  html  
    TCGAanalyze_Filtering                   html  
    TCGAanalyze_LevelTab                    html  
    TCGAanalyze_Normalization               html  
    TCGAanalyze_Preprocessing               html  
    TCGAanalyze_SurvivalKM                  html  
    TCGAanalyze_survival                    html  
    TCGAbiolinks                            html  
    TCGAdownload                            html  
    TCGAprepare                             html  
    TCGAprepare_Affy                        html  
    TCGAprepare_elmer                       html  
    TCGAquery                               html  
    TCGAquery_Investigate                   html  
    TCGAquery_MatchedCoupledSampleTypes     html  
    TCGAquery_SampleTypes                   html  
    TCGAquery_Social                        html  
    TCGAquery_Version                       html  
    TCGAquery_clinic                        html  
    TCGAquery_clinicFilt                    html  
    TCGAquery_integrate                     html  
    TCGAquery_maf                           html  
    TCGAquery_samplesfilter                 html  
    TCGAquery_subtype                       html  
    TCGAvisualize_BarPlot                   html  
    TCGAvisualize_EAbarplot                 html  
    TCGAvisualize_Heatmap                   html  
    TCGAvisualize_PCA                       html  
    TCGAvisualize_SurvivalCoxNET            html  
    TCGAvisualize_Tables                    html  
    TCGAvisualize_meanMethylation           html  
    TCGAvisualize_mutation                  html  
    TCGAvisualize_oncoprint                 html  
    TCGAvisualize_profilePlot               html  
    TCGAvisualize_starburst                 html  
    batch.info                              html  
    calculate.pvalues                       html  
    clinBRCA                                html  
    clinical_data_site_cancer               html  
    dataBRCA                                html  
    dataDEGsFiltLevel                       html  
    dataREAD                                html  
    dataREAD_df                             html  
    diffmean                                html  
    gender_BRCA                             html  
    geneInfo                                html  
    ggbiplot                                html  
    stage_BRCA                              html  
    tabDEGsTFPubmed                         html  
    tabPackage1                             html  
    tabPackage2                             html  
    tabPackageKey                           html  
    tabSurvKMcompleteDEGs                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCGAbiolinks)
Making 'packages.html' ... done