Package: webbioc
Version: 1.44.0
Date: 2009-02-05
Title: Bioconductor Web Interface
Author: Colin A. Smith <colin@colinsmith.org>
Maintainer: Colin A. Smith <colin@colinsmith.org>
Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue
Imports: multtest, qvalue, stats, utils, BiocInstaller
SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm
Description: An integrated web interface for doing microarray analysis
using several of the Bioconductor packages. It is intended to
be deployed as a centralized bioinformatics resource for use
by many users. (Currently only Affymetrix oligonucleotide
analysis is supported.)
License: GPL (>= 2)
URL: http://www.bioconductor.org/
LazyLoad: yes
biocViews: Infrastructure, Microarray, OneChannel,
DifferentialExpression
NeedsCompilation: no
Packaged: 2016-05-04 02:39:29 UTC; biocbuild
Package: CancerMutationAnalysis
Type: Package
Title: Cancer mutation analysis
Version: 1.14.0
Author: Giovanni Parmigiani, Simina M. Boca
Maintainer: Simina M. Boca <smb310@georgetown.edu>
Imports: AnnotationDbi, limma, methods, stats
Depends: R (>= 2.10.0), qvalue
Suggests: KEGG.db
Description: This package implements gene and gene-set level analysis
methods for somatic mutation studies of cancer. The gene-level
methods distinguish between driver genes (which play an active
role in tumorigenesis) and passenger genes (which are mutated
in tumor samples, but have no role in tumorigenesis) and
incorporate a two-stage study design. The gene-set methods
implement a patient-oriented approach, which calculates
gene-set scores for each sample, then combines them across
samples; a gene-oriented approach which uses the Wilcoxon test
is also provided for comparison.
License: GPL (>= 2) + file LICENSE
LazyLoad: yes
biocViews: Genetics, Software
NeedsCompilation: yes
Packaged: 2016-05-04 04:30:53 UTC; biocbuild
Package: ChimpHumanBrainData
Type: Package
Title: Chimp and human brain data package
Version: 1.10.0
Date: 2013-11-04
Author: Roman Jaksik, Naomi Altman, and Sean Davis
Maintainer: Sean Davis <sdavis2@mail.nih.gov>
Description: This data package contains chimp and human brain data extracted from the ArrayExpress
accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It
is a useful dataset for tutorials.
Depends: affy, qvalue, limma, hexbin, statmod
License: MIT
biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data,
MicroarrayData, TissueMicroarrayData, GEO
NeedsCompilation: no
Packaged: 2016-05-07 20:45:06 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: anota
Version: 1.20.0
Date: 2011-03-03
Title: ANalysis Of Translational Activity (ANOTA).
Author: Ola Larsson <ola.larsson@ki.se>, Nahum Sonenberg
<nahum.sonenberg@mcgill.ca>, Robert Nadon
<robert.nadon@mcgill.ca>
Maintainer: Ola Larsson <ola.larsson@ki.se>
Description: Genome wide studies of translational control is emerging
as a tool to study verious biological conditions. The output
from such analysis is both the mRNA level (e.g. cytosolic mRNA
level) and the levl of mRNA actively involved in translation
(the actively translating mRNA level) for each mRNA. The
standard analysis of such data strives towards identifying
differential translational between two or more sample classes -
i.e. differences in actively translated mRNA levels that are
independent of underlying differences in cytosolic mRNA levels.
This package allows for such analysis using partial variances
and the random variance model. As 10s of thousands of mRNAs are
analyzed in parallell the library performs a number of tests to
assure that the data set is suitable for such analysis.
Imports: multtest, qvalue
Depends: qvalue
LazyData: yes
LazyLoad: yes
License: GPL-3
biocViews: GeneExpression, DifferentialExpression, Microarray,
Sequencing
NeedsCompilation: no
Packaged: 2016-05-04 04:02:26 UTC; biocbuild
providing 
.