Package: dyebiasexamples
Version: 1.12.0
Date: 2 March 2016
Title: Example data for the dyebias package, which implements the
GASSCO method.
Author: Philip Lijnzaad and Thanasis Margaritis
Description: Data for the dyebias package, consisting of 4 self-self
hybrizations of self-spotted yeast slides, as well as data
from Array Express accession E-MTAB-32
Maintainer: Philip Lijnzaad <plijnzaad@gmail.com>
License: GPL-3
Depends: R (>= 1.4.1), marray, GEOquery
Suggests: dyebias, convert, Biobase
URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad
biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData,
TwoChannelData, ArrayExpress
NeedsCompilation: no
Packaged: 2016-05-07 20:16:40 UTC; biocbuild
Package: SCAN.UPC
Type: Package
Title: Single-channel array normalization (SCAN) and Universal
exPression Codes (UPC)
Version: 2.14.0
Author: Stephen R. Piccolo and Andrea H. Bild and W. Evan Johnson
Maintainer: Stephen R. Piccolo <stephen_piccolo@byu.edu>
Description: SCAN is a microarray normalization method to facilitate
personalized-medicine workflows. Rather than processing
microarray samples as groups, which can introduce biases and
present logistical challenges, SCAN normalizes each sample
individually by modeling and removing probe- and array-specific
background noise using only data from within each array. SCAN
can be applied to one-channel (e.g., Affymetrix) or two-channel
(e.g., Agilent) microarrays. The Universal exPression Codes
(UPC) method is an extension of SCAN that estimates whether a
given gene/transcript is active above background levels in a
given sample. The UPC method can be applied to one-channel or
two-channel microarrays as well as to RNA-Seq read counts.
Because UPC values are represented on the same scale and have
an identical interpretation for each platform, they can be used
for cross-platform data integration.
License: MIT
Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva
Suggests: pd.hg.u95a
Imports: utils, methods, MASS, tools, IRanges
URL: http://bioconductor.org, http://jlab.bu.edu/software/scan-upc
biocViews: Software, Microarray, Preprocessing, RNASeq, TwoChannel,
OneChannel
NeedsCompilation: no
Packaged: 2016-05-04 04:44:11 UTC; biocbuild
Package: DrugVsDisease
Type: Package
Title: Comparison of disease and drug profiles using Gene set
Enrichment Analysis
Version: 2.12.0
Date: 2015-04-13
Author: C. Pacini
Maintainer: j. Saez-Rodriguez <saezrodriguez@ebi.ac.uk>
Description: This package generates ranked lists of differential gene
expression for either disease or drug profiles. Input data can
be downloaded from Array Express or GEO, or from local CEL
files. Ranked lists of differential expression and associated
p-values are calculated using Limma. Enrichment scores
(Subramanian et al. PNAS 2005) are calculated to a reference
set of default drug or disease profiles, or a set of custom
data supplied by the user. Network visualisation of significant
scores are output in Cytoscape format.
LazyData: yes
LazyLoad: yes
License: GPL-3
Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue
Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable
biocViews: Microarray, GeneExpression, Clustering
NeedsCompilation: no
Packaged: 2016-05-05 03:46:41 UTC; biocbuild
Package: GEOmetadb
Type: Package
Title: A compilation of metadata from NCBI GEO
Version: 1.32.2
Date: 2016-04-14
Depends: GEOquery, RSQLite
Suggests: knitr, rmarkdown, dplyr, tm, wordcloud
Author: Jack Zhu and Sean Davis
Maintainer: Jack Zhu <zhujack@mail.nih.gov>
biocViews: Infrastructure
Description: The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 .
URL: http://gbnci.abcc.ncifcrf.gov/geo/
VignetteBuilder: knitr
License: Artistic-2.0
NeedsCompilation: no
Packaged: 2016-05-16 01:57:14 UTC; biocbuild
Package: GSE62944
Title: GEO accession data GSE62944 as an ExpressionSet
Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal
samples across 24 cancer types and made them available as GEO accession
[GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944).
GSE62944 data have been parsed into an ExpressionSet object available
in ExperimentHub.
Version: 1.0.0
Author: Sonali Arora
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html
biocViews: ExperimentData, Genome, DNASeqData, RNASeqData
Depends: Biobase, GEOquery
Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle
License: Artistic-2.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-07 21:11:04 UTC; biocbuild
providing 
.