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Last data update: 2014.03.03

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RUVSeq : Remove Unwanted Variation from RNA-Seq Data

Package: RUVSeq
Version: 1.6.2
Title: Remove Unwanted Variation from RNA-Seq Data
Description: This package implements the remove unwanted variation
(RUV) methods of Risso et al. (2014) for the normalization of
RNA-Seq read counts between samples.
Authors@R: c(person("Davide", "Risso", email = "risso.davide@gmail.com",
role = c("aut", "cre", "cph")),
person("Sandrine", "Dudoit", role = "aut"),
person("Lorena", "Pantano", role = "ctb"),
person("Kamil", "Slowikowski", role = "ctb"))
Author: Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Lorena Pantano [ctb], Kamil Slowikowski [ctb]
Maintainer: Davide Risso <risso.davide@gmail.com>
Date: 04-15-2014
Imports: methods, MASS
Depends: Biobase, EDASeq (>= 1.99.1), edgeR
Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
VignetteBuilder: knitr
License: Artistic-2.0
LazyLoad: yes
biocViews: DifferentialExpression, Preprocessing, RNASeq, Software
URL: https://github.com/drisso/RUVSeq
BugReports: https://github.com/drisso/RUVSeq/issues
NeedsCompilation: no
Packaged: 2016-05-16 04:35:28 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DifferentialExpression, Preprocessing, RNASeq, Software
● 3 images, 6 functions, 0 datasets
● Reverse Depends: 0

metaseqR : An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Package: metaseqR
Type: Package
Title: An R package for the analysis and result reporting of RNA-Seq
data by combining multiple statistical algorithms.
Author: Panagiotis Moulos <moulos@fleming.gr>
Maintainer: Panagiotis Moulos <moulos@fleming.gr>
Depends: R (>= 2.13.0), EDASeq, DESeq, limma, qvalue
Imports: edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots,
corrplot, vsn, brew, rjson, log4r
Suggests: BiocGenerics, GenomicRanges, rtracklayer, Rsamtools,
survcomp, VennDiagram, knitr, zoo, RUnit, BiocInstaller,
BSgenome, RSQLite
Enhances: parallel, TCC, RMySQL
Description: Provides an interface to several normalization and
statistical testing packages for RNA-Seq gene expression data.
Additionally, it creates several diagnostic plots, performs
meta-analysis by combinining the results of several statistical
tests and reports the results in an interactive way.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
URL: http://www.fleming.gr
biocViews: Software, GeneExpression, DifferentialExpression,
WorkflowStep, Preprocessing, QualityControl, Normalization,
ReportWriting, RNASeq
VignetteBuilder: knitr
Authors@R: c(person(given="Panagiotis", family="Moulos",
email="moulos@fleming.gr", role=c("aut", "cre")))
Version: 1.12.2
Date: 2016-04-04
Collate: 'metaseqr.annotation.R' 'metaseqr.argcheck.R'
'metaseqr.count.R' 'metaseqr-data.R' 'metaseqr.export.R'
'metaseqr.filter.R' 'metaseqr.json.R' 'metaseqr.main.R'
'metaseqr.meta.R' 'metaseqr.norm.R' 'metaseqR-package.R'
'metaseqr.plot.R' 'metaseqr.query.R' 'metaseqr.sim.R'
'metaseqr.stat.R' 'metaseqr.util.R' 'zzz.R'
NeedsCompilation: no
Packaged: 2016-05-16 04:30:26 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DifferentialExpression, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, ReportWriting, Software, WorkflowStep
● 0 images, 126 functions, 6 datasets
● Reverse Depends: 0