Package: curatedBreastData
Type: Package
Title: Curated breast gene expression data with survival and treatment
information
Version: 1.4.0
Date: 2015-03-02
Author: Katie Planey
Maintainer: Katie Planey <katie.planey@gmail.com>
Depends: R (>= 3.0.0), ggplot2, impute, XML, Biobase, BiocStyle
biocViews: GeneExpression, Microarray, ExperimentData,
ReproducibleResearch
Description: Curated breast cancer S4 ExpresionSet datasets that all
contain at least one type of outcomes variable and treatment
information (minimum level: whether they had chemotherapy and
whether they had hormonal therapy). Includes code to
post-process these datasets.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-05-07 20:52:27 UTC; biocbuild
Package: HCsnip
Type: Package
Title: Semi-supervised adaptive-height snipping of the Hierarchical
Clustering tree
Version: 1.12.0
Author: Askar Obulkasim
Maintainer: Askar Obulkasim <askar703@gmail.com>
Description: Decompose given hierarchical clustering tree into
non-overlapping clusters in a semi-supervised way by using
available patients follow-up information as guidance. Contains
functions for snipping HC tree, various cluster quality
evaluation criteria, assigning new patients to one of the two
given HC trees, testing the significance of clusters with
permutation argument and clusters visualization using sample's
molecular entropy.
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 2.10.0), survival, coin, fpc, clusterRepro, impute, randomForestSRC, sm, sigaR, Biobase
Packaged: 2016-05-04 04:53:31 UTC; biocbuild
biocViews: Microarray, aCGH, GeneExpression, Clustering
NeedsCompilation: no
Package: TIN
Type: Package
Title: Transcriptome instability analysis
Version: 1.4.1
Date: 2014-07-14
Author: Bjarne Johannessen, Anita Sveen and Rolf I. Skotheim
Maintainer: Bjarne Johannessen <bjajoh@rr-research.no>
VignetteBuilder: knitr
Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix
Imports: WGCNA, squash, stringr
Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics
biocViews: ExonArray, Microarray, GeneExpression, AlternativeSplicing,
Genetics, DifferentialSplicing
Description: The TIN package implements a set of tools for
transcriptome instability analysis based on exon expression
profiles. Deviating exon usage is studied in the context of
splicing factors to analyse to what degree transcriptome
instability is correlated to splicing factor expression. In the
transcriptome instability correlation analysis, the data is
compared to both random permutations of alternative splicing
scores and expression of random gene sets.
License: Artistic-2.0
NeedsCompilation: no
Packaged: 2016-05-16 05:19:23 UTC; biocbuild
Package: CGHcall
Type: Package
Title: Calling aberrations for array CGH tumor profiles.
Version: 2.34.0
Date: 2014-02-25
Author: Mark van de Wiel, Sjoerd Vosse
Maintainer: Mark van de Wiel <mark.vdwiel@vumc.nl>
Depends: R (>= 2.0.0), impute (>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall
Description: Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.
License: GPL (http://www.gnu.org/copyleft/gpl.html)
biocViews: Microarray,Preprocessing,Visualization
NeedsCompilation: no
Packaged: 2016-05-04 03:02:20 UTC; biocbuild
providing 
.