metaseqR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see metaseqR (see replacement metaseqR2).

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

DOI: 10.18129/B9.bioc.metaseqR

Bioconductor version: 3.12

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.

Author: Panagiotis Moulos <moulos at fleming.gr>

Maintainer: Panagiotis Moulos <moulos at fleming.gr>

Citation (from within R, enter citation("metaseqR")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("metaseqR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("metaseqR")

RNA-Seq data analysis using mulitple statistical algorithms with metaseqR PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, ReportWriting, Software, WorkflowStep

Version 1.30.0

In Bioconductor since BioC 2.14 (R-3.1) (10 years)

License GPL (>= 3)

Depends R (>= 3.4.0), EDASeq, DESeq, limma, qvalue

Imports edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots, corrplot, vsn, brew, rjson, log4r

System Requirements

URL http://www.fleming.gr

Suggests BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager, BSgenome, RSQLite

Linking To

Enhances parallel, TCC, RMySQL

Depends On Me

Imports Me

Suggests Me

Links To Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package metaseqR_1.30.0.tar.gz

Windows Binary metaseqR_1.30.0.zip

macOS 10.13 (High Sierra) metaseqR_1.30.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/metaseqR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metaseqR

Package Short Url https://bioconductor.org/packages/metaseqR/

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Old Source Packages for BioC 3.12 Source Archive