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DESCRIPTION
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DESCRIPTION
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Package: TCGAbiolinks
Type: Package
Title: TCGAbiolinks: An R/Bioconductor package for integrative analysis with
TCGA data
Version: 2.3.11
Date: 2016-12-7
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 <[email protected]>,
Tiago Chedraoui Silva <[email protected]>
Depends:
R (>= 3.2)
Imports:
downloader (>= 0.4),
GGally,
grDevices,
graphics,
tibble,
GenomicRanges,
XML (>= 3.98.0),
Biobase,
affy,
xtable,
data.table,
EDASeq (>= 2.0.0),
edgeR (>= 3.0.0),
jsonlite (>= 1.0.0),
plyr,
knitr,
methods,
biomaRt,
gplots,
ggplot2,
ggthemes,
survival,
stringr (>= 1.0.0),
IRanges,
scales,
rvest (>= 0.3.0),
stats,
utils,
dnet,
igraph,
supraHex,
S4Vectors,
ComplexHeatmap (>= 1.10.2),
R.utils,
SummarizedExperiment (>= 1.4.0),
limma,
genefilter,
ConsensusClusterPlus,
readr,
RColorBrewer,
doParallel,
dplyr,
clusterProfiler,
pathview,
parallel,
xml2,
httr (>= 1.2.1),
parmigene,
matlab,
circlize,
ggrepel (>= 0.6.3)
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